| Order | Family | Species | Status | FB name | Name |
| Characiformes | Anostomidae | Abramites hypselonotus | native | Marbled headstander | Sardina |
| Characiformes | Characidae | Acestrocephalus boehlkei | native | Dientón | |
| Characiformes | Acestrorhynchidae | Acestrorhynchus abbreviatus | native | ||
| Characiformes | Acestrorhynchidae | Acestrorhynchus falcirostris | native | Dientón | |
| Pleuronectiformes | Achiridae | Achirus mazatlanus | native | Mazatlan sole | Lenguadito |
| Perciformes | Cichlidae | Aequidens rivulatus | native | Green terror | Vieja |
| Perciformes | Cichlidae | Aequidens sapayensis | endemic | Sapayo cichlid | Vieja |
| Perciformes | Cichlidae | Aequidens tetramerus | native | Saddle cichlid | Vieja |
| Siluriformes | Doradidae | Agamyxis pectinifrons | misidentification | Whitebarred catfish | Bagre hueso |
| Siluriformes | Auchenipteridae | Ageneiosus inermis | native | Manduba | |
| Siluriformes | Auchenipteridae | Ageneiosus marmoratus | native | Bottlenose catfish | |
| Siluriformes | Auchenipteridae | Ageneiosus ucayalensis | native | ||
| Siluriformes | Auchenipteridae | Ageneiosus vittatus | native | ||
| Characiformes | Characidae | Agoniates anchovia | native | Sardina | |
| Mugiliformes | Mugilidae | Agonostomus monticola | native | Mountain mullet | Lisa |
| Siluriformes | Aspredinidae | Amaralia hypsiura | native | Carachita | |
| Siluriformes | Doradidae | Anadoras grypus | native | Bagre hueso | |
| Clupeiformes | Engraulidae | Anchoa curta | native | Short anchovy | Pelada |
| Clupeiformes | Engraulidae | Anchoa spinifer | native | Spicule anchovy | Colorada |
| Siluriformes | Loricariidae | Ancistrus clementinae | endemic | Raspabalsa | |
| Siluriformes | Loricariidae | Ancistrus occidentalis | endemic | Carachama | |
| Pleuronectiformes | Achiridae | Apionichthys menezesi | native | ||
| Pleuronectiformes | Achiridae | Apionichthys nattereri | native | Lenguado | |
| Pleuronectiformes | Achiridae | Apionichthys seripierriae | native | ||
| Perciformes | Cichlidae | Apistogramma cruzi | native | Vieja | |
| Perciformes | Cichlidae | Apistogramma payaminonis | endemic | Vieja | |
| Siluriformes | Loricariidae | Apistoloricaria condei | native | Carachama | |
| Gymnotiformes | Apteronotidae | Apteronotus albifrons | native | Black ghost | Anguila |
| Osteoglossiformes | Arapaimidae | Arapaima gigas | native | Arapaima | Paiche |
| Siluriformes | Astroblepidae | Astroblepus boulengeri | native | Preñadilla | |
| Siluriformes | Astroblepidae | Astroblepus brachycephalus | native | ||
| Siluriformes | Astroblepidae | Astroblepus chimborazoi | native | ||
| Siluriformes | Astroblepidae | Astroblepus chotae | native | Preñadilla | |
| Siluriformes | Astroblepidae | Astroblepus cyclopus | native | Preñadilla | |
| Siluriformes | Astroblepidae | Astroblepus eigenmanni | native | ||
| Siluriformes | Astroblepidae | Astroblepus festae | native | Preñadilla | |
| Siluriformes | Astroblepidae | Astroblepus fissidens | native | Preñadilla | |
| Siluriformes | Astroblepidae | Astroblepus mindoense | native | Preñadilla | |
| Siluriformes | Astroblepidae | Astroblepus pholeter | endemic | ||
| Siluriformes | Astroblepidae | Astroblepus prenadillus | native | ||
| Siluriformes | Astroblepidae | Astroblepus regani | native | ||
| Siluriformes | Astroblepidae | Astroblepus theresiae | native | ||
| Siluriformes | Astroblepidae | Astroblepus ubidiai | native | Preñadilla | |
| Siluriformes | Astroblepidae | Astroblepus vaillanti | native | Preñadilla bagrecito | |
| Siluriformes | Astroblepidae | Astroblepus whymperi | native | ||
| Characiformes | Characidae | Astyanax bimaculatus | native | Twospot astyanax | Sardinita |
| Characiformes | Characidae | Astyanax festae | native | Sardinita | |
| Siluriformes | Auchenipteridae | Auchenipterus ambyiacus | native | Barbudo | |
| Siluriformes | Auchenipteridae | Auchenipterus brachyurus | native | Barbudo | |
| Perciformes | Gobiidae | Awaous banana | native | River goby | Lameplato |
| Siluriformes | Ariidae | Bagre pinnimaculatus | native | Red sea catfish | Bagre |
| Batrachoidiformes | Batrachoididae | Batrachoides pacifici | native | Pacific toadfish | Bruja sapo |
| Siluriformes | Pseudopimelodidae | Batrochoglanis transmontanus | native | Barbudo negro | |
| Characiformes | Ctenoluciidae | Boulengerella maculata | native | Spotted pike-characin | Picudo |
| Characiformes | Characidae | Brachychalcinus nummus | native | Sardina | |
| Gymnotiformes | Hypopomidae | Brachyhypopomus beebei | native | ||
| Gymnotiformes | Hypopomidae | Brachyhypopomus brevirostris | native | Bluntnose knifefish | Anguila |
| Gymnotiformes | Hypopomidae | Brachyhypopomus pinnicaudatus | native | ||
| Siluriformes | Pimelodidae | Brachyplatystoma filamentosum | native | Kumakuma | Bagre blanco |
| Siluriformes | Pimelodidae | Brachyplatystoma juruense | questionable | Zebra catfish | Bagre |
| Siluriformes | Pimelodidae | Brachyplatystoma platynemum | native | Slobbering catfish | |
| Siluriformes | Pimelodidae | Brachyplatystoma rousseauxii | native | ||
| Siluriformes | Pimelodidae | Brachyplatystoma vaillantii | native | Laulao catfish | Bagre |
| Siluriformes | Callichthyidae | Brochis multiradiatus | native | Hognosed brochis | Caracha |
| Siluriformes | Callichthyidae | Brochis splendens | native | Emerald catfish | Caracha |
| Characiformes | Characidae | Brycon alburnus | native | Sábalo | |
| Characiformes | Characidae | Brycon atrocaudatus | native | Sábalo | |
| Characiformes | Characidae | Brycon coxeyi | native | Sábalo | |
| Characiformes | Characidae | Brycon dentex | native | Sábalo | |
| Characiformes | Characidae | Brycon falcatus | misidentification | ||
| Characiformes | Characidae | Brycon melanopterus | native | Sábalo | |
| Characiformes | Characidae | Brycon oligolepis | native | Sábalo | |
| Characiformes | Characidae | Brycon pesu | native | Mourning tetra | Sábalo |
| Characiformes | Characidae | Brycon posadae | native | ||
| Characiformes | Characidae | Bryconacidnus ellisi | native | Sardina | |
| Characiformes | Characidae | Bryconamericus brevirostris | native | Sabaleta | |
| Characiformes | Characidae | Bryconamericus carlosi | native | ||
| Characiformes | Characidae | Bryconamericus peruanus | native | Sardina | |
| Characiformes | Characidae | Bryconamericus scleroparius | native | Sardina | |
| Characiformes | Characidae | Bryconamericus simus | native | Sardina | |
| Perciformes | Cichlidae | Bujurquina zamorensis | endemic | Mojarra | |
| Siluriformes | Aspredinidae | Bunocephalus aleuropsis | native | ||
| Siluriformes | Aspredinidae | Bunocephalus bifidus | native | Carachita | |
| Siluriformes | Aspredinidae | Bunocephalus knerii | native | Ecuador banjo catfish | Carachita |
| Siluriformes | Aspredinidae | Bunocephalus verrucosus | native | Bark catfish | Ciego |
| Characiformes | Chilodontidae | Caenotropus labyrinthicus | native | Sardina | |
| Siluriformes | Callichthyidae | Callichthys callichthys | native | Cascarudo | Caracha |
| Siluriformes | Pimelodidae | Calophysus macropterus | questionable | Zamurito | Bagre |
| Perciformes | Cichlidae | Caquetaia myersi | native | Vieja | |
| Carcharhiniformes | Carcharhinidae | Carcharhinus leucas | native | Bull shark | Cazón |
| Siluriformes | Ariidae | Cathorops fuerthii | native | Congo sea catfish | Bagre |
| Siluriformes | Ariidae | Cathorops steindachneri | native | Steindachner's sea catfish | Bagre baboso |
| Siluriformes | Ariidae | Cathorops tuyra | native | Besudo sea catfish | |
| Siluriformes | Auchenipteridae | Centromochlus perugiae | native | Barbudito | |
| Characiformes | Characidae | Ceratobranchia elatior | native | Sardina | |
| Siluriformes | Cetopsidae | Cetopsis amphiloxa | native | Ciego | |
| Siluriformes | Cetopsidae | Cetopsis candiru | native | Ciego | |
| Siluriformes | Cetopsidae | Cetopsis coecutiens | native | Ciego | |
| Siluriformes | Cetopsidae | Cetopsis montana | native | ||
| Siluriformes | Cetopsidae | Cetopsis parma | native | ||
| Siluriformes | Cetopsidae | Cetopsis plumbea | native | Ciego | |
| Siluriformes | Heptapteridae | Cetopsorhamdia orinoco | native | Barbudo | |
| Siluriformes | Heptapteridae | Cetopsorhamdia phantasia | endemic | Barbudo | |
| Siluriformes | Loricariidae | Chaetostoma aequinoctiale | endemic | Carachama | |
| Siluriformes | Loricariidae | Chaetostoma breve | endemic | Carachama | |
| Siluriformes | Loricariidae | Chaetostoma dermorhynchum | native | Carachama | |
| Siluriformes | Loricariidae | Chaetostoma fischeri | native | Carachama | |
| Siluriformes | Loricariidae | Chaetostoma marginatum | native | Raspabalsa | |
| Siluriformes | Loricariidae | Chaetostoma microps | native | Raspabalsa | |
| Characiformes | Crenuchidae | Characidium boehlkei | native | Sardina | |
| Characiformes | Crenuchidae | Characidium purpuratum | native | Sardina | |
| Characiformes | Crenuchidae | Characidium steindachneri | native | Sardina | |
| Characiformes | Characidae | Charax tectifer | misidentification | Sardinita | |
| Siluriformes | Pimelodidae | Cheirocerus eques | native | Barbudo | |
| Characiformes | Chilodontidae | Chilodus punctatus | native | Spotted headstander | Sardina |
| Perciformes | Cichlidae | Cichlasoma festae | native | Guayas cichlid | Vieja |
| Perciformes | Cichlidae | Cichlasoma ornatum | native | Macho | |
| Pleuronectiformes | Paralichthyidae | Citharichthys gilberti | native | Bigmouth sanddab | Lenguado |
| Characiformes | Characidae | Clupeacharax anchoveoides | native | Sardina | |
| Characiformes | Lebiasinidae | Copeina guttata | native | Redspotted tetra | Sardina |
| Siluriformes | Loricariidae | Cordylancistrus platycephalus | endemic | Carachama | |
| Siluriformes | Callichthyidae | Corydoras acutus | native | Blacktop corydoras | Caracha |
| Siluriformes | Callichthyidae | Corydoras arcuatus | native | Skunk corydoras | Caracha |
| Siluriformes | Callichthyidae | Corydoras atropersonatus | native | Caracha | |
| Siluriformes | Callichthyidae | Corydoras leopardus | native | Caracha | |
| Siluriformes | Callichthyidae | Corydoras leucomelas | native | False spotted catfish | Caracha |
| Siluriformes | Callichthyidae | Corydoras napoensis | native | Caracha | |
| Siluriformes | Callichthyidae | Corydoras orphnopterus | native | Caracha | |
| Siluriformes | Callichthyidae | Corydoras pastazensis | native | Pastaza corydoras | Caracha |
| Siluriformes | Callichthyidae | Corydoras stenocephalus | native | ||
| Siluriformes | Callichthyidae | Corydoras zygatus | native | Black band catfish | |
| Characiformes | Characidae | Creagrutus amoenus | native | Sardina | |
| Characiformes | Characidae | Creagrutus barrigai | native | ||
| Characiformes | Characidae | Creagrutus flavescens | native | ||
| Characiformes | Characidae | Creagrutus gephyrus | native | Sardina | |
| Characiformes | Characidae | Creagrutus gracilis | native | ||
| Characiformes | Characidae | Creagrutus kunturus | native | ||
| Characiformes | Characidae | Creagrutus muelleri | native | Sardina | |
| Perciformes | Cichlidae | Crenicara punctulatum | native | Checkerboard cichlid | Vieja |
| Perciformes | Cichlidae | Crenicichla anthurus | native | ||
| Perciformes | Cichlidae | Crenicichla cincta | native | Chui | |
| Perciformes | Cichlidae | Crenicichla proteus | native | Chui | |
| Perciformes | Cichlidae | Crenicichla sedentaria | native | Chui | |
| Siluriformes | Loricariidae | Crossoloricaria rhami | native | Carachama | |
| Characiformes | Curimatidae | Curimata aspera | native | Boquiche | |
| Characiformes | Curimatidae | Curimata vittata | misidentification | Boquiche | |
| Characiformes | Curimatidae | Curimatella meyeri | native | Boquilla | |
| Characiformes | Curimatidae | Curimatopsis macrolepis | native | Shinyscaled curimata | Boquilla |
| Characiformes | Cynodontidae | Cynodon gibbus | native | Perrito | |
| Characiformes | Curimatidae | Cyphocharax gouldingi | native | ||
| Characiformes | Curimatidae | Cyphocharax laticlavius | native | ||
| Characiformes | Curimatidae | Cyphocharax notatus | native | ||
| Characiformes | Curimatidae | Cyphocharax pantostictos | native | Boquiche | |
| Characiformes | Curimatidae | Cyphocharax spiluropsis | native | ||
| Characiformes | Curimatidae | Cyphocharax vexillapinnus | native | ||
| Gymnotiformes | Sternopygidae | Distocyclus conirostris | native | Anguila | |
| Siluriformes | Doradidae | Doras punctatus | native | Bagre hueso | |
| Perciformes | Eleotridae | Dormitator latifrons | native | Pacific fat sleeper | Chalaco |
| Siluriformes | Pimelodidae | Duopalatinus peruanus | questionable | ||
| Gymnotiformes | Sternopygidae | Eigenmannia virescens | native | Glass knifefish | Anguila |
| Perciformes | Eleotridae | Eleotris picta | native | Spotted sleeper | Mongolo |
| Perciformes | Eleotridae | Eleotris pisonis | native | Spinycheek sleeper | |
| Characiformes | Characidae | Engraulisoma taeniatum | native | Sardinita | |
| Siluriformes | Aspredinidae | Ernstichthys intonsus | native | Carachita | |
| Siluriformes | Aspredinidae | Ernstichthys megistus | native | ||
| Perciformes | Gerreidae | Eucinostomus currani | native | Pacific flagfin mojarra | |
| Perciformes | Gerreidae | Eucinostomus gracilis | native | Graceful mojarra | Mojarra leiro |
| Siluriformes | Pimelodidae | Exallodontus aguanai | questionable | ||
| Siluriformes | Loricariidae | Farlowella knerii | native | Palito | |
| Siluriformes | Loricariidae | Farlowella nattereri | native | ||
| Siluriformes | Loricariidae | Farlowella odontotumulus | native | ||
| Siluriformes | Loricariidae | Farlowella oxyrryncha | native | Palito | |
| Siluriformes | Heptapteridae | Gladioglanis conquistador | native | ||
| Gobiesociformes | Gobiesocidae | Gobiesox multitentaculus | native | Fondero | |
| Perciformes | Gobiidae | Gobioides peruanus | native | Peruvian eelgoby | Burrulango |
| Perciformes | Eleotridae | Gobiomorus maculatus | native | Pacific sleeper | Cawa |
| Characiformes | Characidae | Grundulus quitoensis | native | ||
| Gymnotiformes | Gymnotidae | Gymnotus carapo | native | Banded knifefish | Anguila |
| Gymnotiformes | Gymnotidae | Gymnotus esmeraldas | native | ||
| Gymnotiformes | Gymnotidae | Gymnotus javari | native | ||
| Gymnotiformes | Gymnotidae | Gymnotus tigre | native | ||
| Siluriformes | Doradidae | Hassar orestis | native | Bagre hueso | |
| Siluriformes | Cetopsidae | Helogenes marmoratus | native | Bagre | |
| Siluriformes | Loricariidae | Hemiancistrus annectens | native | Raspabalsa | |
| Siluriformes | Loricariidae | Hemiancistrus fugleri | endemic | Raspabalsa | |
| Siluriformes | Loricariidae | Hemiancistrus hammarlundi | endemic | Raspabalsa | |
| Siluriformes | Loricariidae | Hemiancistrus landoni | native | Raspabalsa | |
| Characiformes | Characidae | Hemibrycon jelskii | misidentification | Sardina | |
| Characiformes | Characidae | Hemibrycon orcesi | native | Sardina | |
| Characiformes | Characidae | Hemibrycon pautensis | native | ||
| Characiformes | Characidae | Hemibrycon polyodon | native | Sardina | |
| Siluriformes | Doradidae | Hemidoras morrisi | native | Bagre hueso | |
| Siluriformes | Pimelodidae | Hemisorubim platyrhynchos | native | Porthole shovelnose catfish | Barbudo |
| Siluriformes | Trichomycteridae | Henonemus punctatus | native | Bagrecito | |
| Perciformes | Cichlidae | Heroina isonycterina | native | ||
| Characiformes | Characidae | Heterocharax macrolepis | native | Sardinita | |
| Siluriformes | Ariidae | Hexanematichthys henni | native | Bagre | |
| Characiformes | Erythrinidae | Hoplerythrinus unitaeniatus | native | Aimara | Sardina |
| Characiformes | Erythrinidae | Hoplias malabaricus | native | Trahira | Guanchiche |
| Characiformes | Erythrinidae | Hoplias microlepis | native | Juanchiche | |
| Siluriformes | Aspredinidae | Hoplomyzon papillatus | native | Carachita | |
| Siluriformes | Callichthyidae | Hoplosternum littorale | native | Hassar | |
| Siluriformes | Heptapteridae | Horiomyzon retropinnatus | native | Barbudo | |
| Characiformes | Cynodontidae | Hydrolycus scomberoides | native | Payara | Dientón |
| Characiformes | Characidae | Hyphessobrycon ecuadorensis | native | Sardinita | |
| Characiformes | Characidae | Hyphessobrycon ecuadoriensis | native | ||
| Characiformes | Characidae | Hyphessobrycon panamensis | native | ||
| Siluriformes | Loricariidae | Hypostomus hemicochliodon | native | ||
| Perciformes | Blenniidae | Hypsoblennius maculipinna | native | ||
| Characiformes | Prochilodontidae | Ichthyoelephas humeralis | native | Bocochico | |
| Characiformes | Characidae | Iguanodectes spilurus | native | Sardina | |
| Siluriformes | Heptapteridae | Imparfinis longicaudus | endemic | Barbudo | |
| Siluriformes | Heptapteridae | Imparfinis stictonotus | native | Barbudo | |
| Characiformes | Characidae | Iotabrycon praecox | native | Sardina | |
| Siluriformes | Loricariidae | Isorineloricaria spinosissima | native | Zucchini catfish | Raspabalsa |
| Siluriformes | Trichomycteridae | Ituglanis laticeps | native | Bagrecito | |
| Characiformes | Characidae | Jupiaba asymmetrica | native | Sardinita | |
| Characiformes | Characidae | Knodus delta | native | Sardinita | |
| Characiformes | Characidae | Knodus gamma | native | Sardinita | |
| Characiformes | Characidae | Knodus septentrionalis | native | ||
| Perciformes | Cichlidae | Laetacara flavilabris | native | Vieja | |
| Siluriformes | Loricariidae | Lamontichthys stibaros | native | Raspabalsa | |
| Characiformes | Characidae | Landonia latidens | native | Sardinita | |
| Characiformes | Lebiasinidae | Lebiasina bimaculata | native | Twospot lebiasina | Guabina |
| Siluriformes | Pimelodidae | Leiarius pictus | questionable | ||
| Characiformes | Anostomidae | Leporinus ecuadorensis | endemic | Ratón | |
| Characiformes | Anostomidae | Leporinus jatuncochi | native | Ratón | |
| Characiformes | Anostomidae | Leporinus pearsoni | native | Septimo | |
| Characiformes | Anostomidae | Leporinus striatus | native | Sardina | |
| Characiformes | Characidae | Leptagoniates steindachneri | native | Sardinita | |
| Siluriformes | Doradidae | Leptodoras acipenserinus | native | Bagre hueso | |
| Clupeiformes | Clupeidae | Lile stolifera | native | Pacific piquitinga | Pelada |
| Siluriformes | Loricariidae | Limatulichthys griseus | native | Carachama | |
| Siluriformes | Loricariidae | Lipopterichthys carrioni | native | Carachama | |
| Siluriformes | Loricariidae | Loricaria simillima | native | Carachama | |
| Siluriformes | Callichthyidae | Megalechis picta | native | Spotted hoplo | Caracha |
| Siluriformes | Callichthyidae | Megalechis thoracata | native | ||
| Siluriformes | Doradidae | Megalodoras uranoscopus | native | Bagre hueso | |
| Siluriformes | Pimelodidae | Megalonema platycephalum | native | Barbudo | |
| Characiformes | Crenuchidae | Melanocharacidium rex | endemic | Sardina | |
| Siluriformes | Pseudopimelodidae | Microglanis pellopterygius | endemic | Barbudo | |
| Siluriformes | Pseudopimelodidae | Microglanis variegatus | endemic | Barbudo | |
| Characiformes | Characidae | Moenkhausia naponis | native | Sardinita | |
| Perciformes | Moronidae | Morone saxatilis | introduced | Striped bass | |
| Mugiliformes | Mugilidae | Mugil cephalus | native | Flathead mullet | Lisa |
| Characiformes | Characidae | Myloplus rubripinnis | native | Redhook myleus | Sardinita |
| Characiformes | Characidae | Mylossoma aureum | native | Palometa | |
| Characiformes | Characidae | Mylossoma duriventre | native | Sabaletín | |
| Siluriformes | Heptapteridae | Nannoglanis fasciatus | endemic | Barbudo | |
| Siluriformes | Loricariidae | Nannoptopoma sternoptychum | native | ||
| Siluriformes | Doradidae | Nemadoras trimaculatus | native | Bagre hueso | |
| Siluriformes | Heptapteridae | Nemuroglanis lanceolatus | native | ||
| Characiformes | Characidae | Odontostilbe ecuadorensis | native | ||
| Characiformes | Characidae | Odontostilbe roloffi | native | Sardinita | |
| Perciformes | Carangidae | Oligoplites saurus | native | Leatherjack | Voladora mascapalo |
| Salmoniformes | Salmonidae | Oncorhynchus mykiss | introduced | Rainbow trout | Trucha arco iris |
| Clupeiformes | Clupeidae | Opisthopterus effulgens | native | Vaqueira longfin herring | |
| Siluriformes | Doradidae | Opsodoras stuebelii | native | Bagre hueso | |
| Perciformes | Cichlidae | Oreochromis mossambicus | not established | Mozambique tilapia | Tilapia |
| Perciformes | Cichlidae | Oreochromis niloticus niloticus | introduced | Nile tilapia | Tilapia |
| Siluriformes | Loricariidae | Otocinclus huaorani | native | ||
| Siluriformes | Doradidae | Oxydoras niger | native | Ripsaw catfish | Bagre hueso |
| Perciformes | Sciaenidae | Pachyurus stewarti | native | ||
| Siluriformes | Loricariidae | Panaqolus albomaculatus | native | Carachama | |
| Siluriformes | Loricariidae | Panaqolus dentex | native | Carachama | |
| Siluriformes | Loricariidae | Panaqolus gnomus | native | Dwarf panaque | |
| Siluriformes | Loricariidae | Panaqolus nocturnus | native | Dusky panaque | |
| Siluriformes | Cetopsidae | Paracetopsis atahualpa | native | ||
| Siluriformes | Cetopsidae | Paracetopsis bleekeri | native | Ciego | |
| Siluriformes | Cetopsidae | Paracetopsis esmeraldas | native | ||
| Rajiformes | Potamotrygonidae | Paratrygon aiereba | native | Discus ray | Raya |
| Characiformes | Parodontidae | Parodon buckleyi | native | Ratón | |
| Characiformes | Parodontidae | Parodon pongoensis | native | Pongo characin | Ratón |
| Clupeiformes | Pristigasteridae | Pellona castelnaeana | native | Amazon pellona | |
| Characiformes | Characidae | Phenacobrycon henni | native | Sardina | |
| Siluriformes | Pimelodidae | Phractocephalus hemioliopterus | native | Redtail catfish | Guacamayo bagre |
| Characiformes | Lebiasinidae | Piabucina astrigata | native | Guaija | |
| Characiformes | Lebiasinidae | Piabucina aureoguttata | native | Guaija | |
| Characiformes | Lebiasinidae | Piabucina elongata | native | Guaija | |
| Siluriformes | Heptapteridae | Pimelodella buckleyi | native | Barbudo | |
| Siluriformes | Heptapteridae | Pimelodella elongata | endemic | Barbudo | |
| Siluriformes | Heptapteridae | Pimelodella grisea | endemic | Barbudo | |
| Siluriformes | Heptapteridae | Pimelodella modestus | endemic | Barbudo | |
| Siluriformes | Pimelodidae | Pimelodina flavipinnis | questionable | ||
| Siluriformes | Pimelodidae | Pimelodus blochii | native | Bloch's catfish | Barbudo |
| Siluriformes | Pimelodidae | Pimelodus jivaro | native | Barbudo | |
| Siluriformes | Pimelodidae | Pimelodus ornatus | native | Barbudo | |
| Siluriformes | Pimelodidae | Pimelodus parvus | native | Barbudo | |
| Siluriformes | Pimelodidae | Pinirampus pirinampu | native | Flatwhiskered catfish | Bagre |
| Perciformes | Sciaenidae | Plagioscion squamosissimus | native | South American silver croaker | Corvina |
| Siluriformes | Pimelodidae | Platynematichthys notatus | questionable | Coroat� | |
| Siluriformes | Pimelodidae | Platysilurus olallae | native | ||
| Siluriformes | Pimelodidae | Platystomatichthys sturio | native | Bagre | |
| Siluriformes | Trichomycteridae | Plectrochilus wieneri | native | Canero | |
| Rajiformes | Potamotrygonidae | Plesiotrygon iwamae | native | Long-tailed river stingray | Raya |
| Perciformes | Haemulidae | Pomadasys bayanus | native | Purplemouth grunt | Roncador corvina |
| Beloniformes | Belonidae | Potamorrhaphis guianensis | native | Lápiz | |
| Characiformes | Characidae | Prionobrama filigera | native | Glass bloodfin | Sardina |
| Clupeiformes | Pristigasteridae | Pristigaster whiteheadi | native | ||
| Characiformes | Prochilodontidae | Prochilodus nigricans | native | Black prochilodus | Bocachico |
| Characiformes | Curimatidae | Psectrogaster amazonica | native | Boquiche | |
| Characiformes | Characidae | Pseudochalceus bohlkei | native | ||
| Characiformes | Characidae | Pseudochalceus lineatus | native | Sardina | |
| Characiformes | Characidae | Pseudochalceus longianalis | native | ||
| Characiformes | Curimatidae | Pseudocurimata boehlkei | native | Nayón | |
| Characiformes | Curimatidae | Pseudocurimata boulengeri | native | Nayón | |
| Characiformes | Curimatidae | Pseudocurimata lineopunctata | native | Nayón | |
| Characiformes | Curimatidae | Pseudocurimata troschelii | native | Boquiche | |
| Siluriformes | Loricariidae | Pseudohemiodon apithanos | native | Caracha | |
| Syngnathiformes | Syngnathidae | Pseudophallus starksii | native | Caballito | |
| Siluriformes | Pseudopimelodidae | Pseudopimelodus pulcher | native | Barbudo | |
| Siluriformes | Pimelodidae | Pseudoplatystoma fasciatum | native | Barred sorubim | Bagre rayado |
| Siluriformes | Pimelodidae | Pseudoplatystoma tigrinum | native | Tiger sorubim | Bagre rayado |
| Cyprinodontiformes | Poeciliidae | Pseudopoecilia festae | native | ||
| Cyprinodontiformes | Poeciliidae | Pseudopoecilia fria | native | Camotillo | |
| Beloniformes | Belonidae | Pseudotylosurus angusticeps | native | Pez lápiz aguja | |
| Siluriformes | Aspredinidae | Pterobunocephalus depressus | native | ||
| Siluriformes | Loricariidae | Pterygoplichthys gibbiceps | native | Leopard pleco | Carachama |
| Siluriformes | Loricariidae | Pterygoplichthys punctatus | native | Corroncho | Carachama |
| Siluriformes | Loricariidae | Pterygoplichthys weberi | native | ||
| Characiformes | Characidae | Pygocentrus nattereri | native | Red piranha | Piraña |
| Characiformes | Lebiasinidae | Pyrrhulina obermulleri | native | ||
| Characiformes | Lebiasinidae | Pyrrhulina semifasciata | native | Sardina | |
| Gymnotiformes | Sternopygidae | Rhabdolichops caviceps | native | Anguila | |
| Gymnotiformes | Sternopygidae | Rhabdolichops eastwardi | native | Anguila | |
| Siluriformes | Loricariidae | Rhadinoloricaria macromystax | native | Carachama | |
| Siluriformes | Heptapteridae | Rhamdia poeyi | native | ||
| Siluriformes | Heptapteridae | Rhamdia quelen | native | Bagre | |
| Characiformes | Cynodontidae | Rhaphiodon vulpinus | native | Biara | Dientón |
| Siluriformes | Doradidae | Rhinodoras boehlkei | native | Bagre hueso | |
| Characiformes | Characidae | Rhoadsia altipinna | native | Sabaleta | |
| Characiformes | Characidae | Rhoadsia minor | native | Sabaleta | |
| Siluriformes | Doradidae | Rhynchodoras woodsi | native | Bagre hueso | |
| Siluriformes | Loricariidae | Rineloricaria jubata | native | Guitarra | |
| Cyprinodontiformes | Rivulidae | Rivulus erberi | endemic | ||
| Cyprinodontiformes | Rivulidae | Rivulus jucundus | endemic | ||
| Cyprinodontiformes | Rivulidae | Rivulus limoncochae | native | Sardinita | |
| Cyprinodontiformes | Rivulidae | Rivulus monticola | native | ||
| Characiformes | Characidae | Roeboides occidentalis | native | Dientón | |
| Characiformes | Parodontidae | Saccodon terminalis | endemic | Sardina | |
| Characiformes | Parodontidae | Saccodon wagneri | native | Roncador | |
| Characiformes | Characidae | Salminus affinis | native | Dama | |
| Characiformes | Characidae | Salminus hilarii | native | Dama | |
| Perciformes | Cichlidae | Satanoperca jurupari | native | Demon eartheater | Vieja |
| Siluriformes | Ariidae | Sciades dowii | native | Brown sea catfish | Bagre |
| Siluriformes | Ariidae | Sciades seemanni | native | Tete sea catfish | Bagre |
| Characiformes | Prochilodontidae | Semaprochilodus insignis | native | Bocachico | |
| Characiformes | Characidae | Serrasalmus elongatus | native | Slender piranha | Piraña |
| Characiformes | Characidae | Serrasalmus rhombeus | native | Redeye piranha | Piraña |
| Perciformes | Gobiidae | Sicydium rosenbergii | endemic | ||
| Siluriformes | Pimelodidae | Sorubim elongatus | native | Slender shovelnose catfish | |
| Siluriformes | Pimelodidae | Sorubim lima | native | Duckbill catfish | Bagre |
| Siluriformes | Pimelodidae | Sorubim maniradii | native | ||
| Siluriformes | Pimelodidae | Sorubimichthys planiceps | native | Firewood catfish | Bagre |
| Gymnotiformes | Hypopomidae | Steatogenys elegans | native | Barred knifefish | Anguila |
| Characiformes | Curimatidae | Steindachnerina bimaculata | native | Boquiche | |
| Characiformes | Curimatidae | Steindachnerina dobula | native | Boquiche | |
| Characiformes | Curimatidae | Steindachnerina guentheri | native | Boquiche | |
| Gymnotiformes | Apteronotidae | Sternarchorhynchus curvirostris | native | Anguila | |
| Gymnotiformes | Sternopygidae | Sternopygus arenatus | native | ||
| Gymnotiformes | Sternopygidae | Sternopygus macrurus | native | Longtail knifefish | Bio del rio |
| Beloniformes | Belonidae | Strongylura exilis | native | Californian needlefish | Aguja brava |
| Beloniformes | Belonidae | Strongylura fluviatilis | native | ||
| Siluriformes | Loricariidae | Sturisoma frenatum | native | Raspabalsa | |
| Siluriformes | Loricariidae | Sturisoma panamense | native | Guitarrera | |
| Synbranchiformes | Synbranchidae | Synbranchus marmoratus | native | Marbled swamp eel | Culebra |
| Batrachoidiformes | Batrachoididae | Thalassophryne amazonica | native | ||
| Characiformes | Gasteropelecidae | Thoracocharax stellatus | native | Spotfin hatchetfish | Volador |
| Siluriformes | Doradidae | Trachydoras steindachneri | native | Bagre hueso | |
| Siluriformes | Trichomycteridae | Trichomycterus bomboizanus | native | ||
| Siluriformes | Trichomycteridae | Trichomycterus knerii | native | Bagrecito | |
| Siluriformes | Trichomycteridae | Trichomycterus taenia | native | Bagrecito | |
| Pleuronectiformes | Achiridae | Trinectes fluviatilis | native | Freshwater sole | Lenguado |
| Characiformes | Characidae | Triportheus albus | native | Pechón | |
| Characiformes | Characidae | Triportheus angulatus | native | Pechón | |
| Siluriformes | Trichomycteridae | Vandellia cirrhosa | native | Candiru | Canero |
| Characiformes | Characidae | Xenurobrycon heterodon | native | Sardina | |
| Siluriformes | Aspredinidae | Xyliphius lepturus | native | Carachita | |
| Siluriformes | Aspredinidae | Xyliphius melanopterus | native | Carachita | |
| Siluriformes | Pimelodidae | Zungaro zungaro | native | Gilded catfish | Bagre blanco |