| Sparidae | Acanthopagrus berda | Picnic seabream | Bitilya | native |
| Ambassidae | Ambassis gymnocephalus | Bald glassy | Langarai | native |
| Ambassidae | Ambassis interrupta | Long-spined glass perchlet | Langaray | native |
| Ambassidae | Ambassis macracanthus | Estuarine glass perchlet | native |
| Ambassidae | Ambassis nalua | Scalloped perchlet | native |
| Ambassidae | Ambassis urotaenia | Banded-tail glassy perchlet | native |
| Anabantidae | Anabas testudineus | Climbing perch | Liwalo | native |
| Anguillidae | Anguilla australis australis | Shortfin eel | Igat | native |
| Anguillidae | Anguilla bicolor bicolor | Indonesian shortfin eel | Igat | native |
| Anguillidae | Anguilla bicolor pacifica | Indian short-finned eel | Igat | native |
| Anguillidae | Anguilla celebesensis | Celebes longfin eel | Igat | native |
| Anguillidae | Anguilla japonica | Japanese eel | Japanese eel | native |
| Anguillidae | Anguilla malgumora | Indonesian longfinned eel | native |
| Anguillidae | Anguilla marmorata | Giant mottled eel | Igat | native |
| Antennariidae | Antennarius biocellatus | Brackishwater frogfish | native |
| Aplocheilidae | Aplocheilus panchax | Blue panchax | Killie | native |
| Apogonidae | Apogon hyalosoma | Humpbacked cardinalfish | Dangat | native |
| Cyprinidae | Aristichthys nobilis | Bighead carp | introduced |
| Ariidae | Arius dispar | Sea catfish | native |
| Ariidae | Arius leptaspis | Salmon catfish | native |
| Ariidae | Arius magatensis | endemic |
| Ariidae | Arius manillensis | Sea catfish | endemic |
| Ariidae | Arius subrostratus | Shovelnose sea catfish | Short nosed catfish | native |
| Ariidae | Arius sumatranus | Goat catfish | native |
| Rivulidae | Austrolebias nigripinnis | Blackfin pearlfish | introduced |
| Gobiidae | Awaous grammepomus | Scribbled goby | Bia | native |
| Gobiidae | Awaous litturatus | native |
| Gobiidae | Awaous melanocephalus | Largesnout goby | Biang bato | native |
| Gobiidae | Awaous ocellaris | Bia | native |
| Cyprinidae | Barbodes collingwoodii | questionable |
| Cyprinidae | Barbonymus gonionotus | Java barb | Tawes | introduced |
| Gobiidae | Bathygobius fuscus | Dusky frillgoby | Bia | native |
| Eleotridae | Belobranchus belobranchus | Throat-spine gudgeon | Batingulo | native |
| Gobiidae | Boleophthalmus boddarti | Boddart's goggle-eyed goby | Bia | native |
| Gobiidae | Brachygobius aggregatus | Schooling bumblebee goby | Bia | native |
| Eleotridae | Bunaka gyrinoides | Greenback gauvina | native |
| Eleotridae | Bunaka pinguis | Boto-bot | native |
| Eleotridae | Butis amboinensis | Olive flathead-gudgeon | Biyang sunog | native |
| Eleotridae | Butis butis | Duckbill sleeper | Pasel | native |
| Eleotridae | Butis gymnopomus | native |
| Eleotridae | Butis koilomatodon | Mud sleeper | native |
| Gobiidae | Caecogobius cryptophthalmus | endemic |
| Gobiidae | Calamiana illota | native |
| Gobiidae | Callogobius hasseltii | Hasselt's goby | Bia | native |
| Gobiidae | Caragobius urolepis | Scaleless worm goby | Bia | native |
| Cyprinidae | Carassius auratus auratus | Goldfish | Tawes | introduced |
| Cyprinidae | Carassius carassius | Crucian carp | Wild goldfish | introduced |
| Carcharhinidae | Carcharhinus leucas | Bull shark | Pating | native |
| Cyprinidae | Catla catla | Catla | introduced |
| Mugilidae | Cestraeus goldiei | Goldie river mullet | Banak | native |
| Mugilidae | Cestraeus oxyrhyncus | Sharp-nosed river mullet | Banak | native |
| Mugilidae | Cestraeus plicatilis | Lobed river mullet | native |
| Channidae | Channa maculata | native |
| Channidae | Channa melasoma | Black snakehead | native |
| Channidae | Channa striata | Snakehead murrel | Anak dalag | native |
| Chanidae | Chanos chanos | Milkfish | Bangus | native |
| Cyprinidae | Cirrhinus cirrhosus | Mrigal | introduced |
| Clariidae | Clarias batrachus | Walking catfish | Hitong batukan | introduced |
| Clariidae | Clarias fuscus | Whitespotted clarias | native |
| Clariidae | Clarias gariepinus | North African catfish | introduced |
| Clariidae | Clarias macrocephalus | Broadhead catfish | Hito | native |
| Clariidae | Clarias meladerma | Blackskin catfish | native |
| Clariidae | Clarias nieuhofii | native |
| Characidae | Colossoma macropomum | Tambaqui | introduced |
| Mugilidae | Crenimugil heterocheilos | Half fringelip mullet | Banak | native |
| Cyprinidae | Ctenopharyngodon idella | Grass carp | not established |
| Cyprinidae | Cyclocheilichthys armatus | native |
| Cynoglossidae | Cynoglossus puncticeps | Speckled tonguesole | Ararali | native |
| Cyprinidae | Cyprinus carpio carpio | Common carp | Karpa | introduced |
| Hemiramphidae | Dermogenys palawanensis | native |
| Hemiramphidae | Dermogenys pusilla | Wrestling halfbeak | Needle gar | native |
| Hemiramphidae | Dermogenys robertsi | native |
| Syngnathidae | Doryichthys boaja | Long-snouted pipefish | native |
| Syngnathidae | Doryichthys martensii | native |
| Muraenidae | Echidna rhodochilus | native |
| Eleotridae | Eleotris acanthopoma | native |
| Eleotridae | Eleotris fusca | Dusky sleeper | Batingulo | native |
| Eleotridae | Eleotris melanosoma | Broadhead sleeper | Ipon | native |
| Elopidae | Elops hawaiensis | Hawaiian ladyfish | Bid-bid | native |
| Serranidae | Epinephelus polystigma | White-dotted grouper | Lapu lapu | native |
| Gobiidae | Eugnathogobius oligactis | native |
| Gobiidae | Favonigobius reichei | Indo-Pacific tropical sand goby | Bia | native |
| Fundulidae | Fundulus heteroclitus heteroclitus | Mummichog | introduced |
| Poeciliidae | Gambusia affinis | Mosquitofish | Isdang canal | introduced |
| Gobiidae | Glossogobius aureus | Golden tank goby | Bia | native |
| Gobiidae | Glossogobius bicirrhosus | Bia | native |
| Gobiidae | Glossogobius celebius | Celebes goby | Biyang bato | native |
| Gobiidae | Glossogobius circumspectus | Bia | native |
| Gobiidae | Glossogobius giuris | Tank goby | Bia | native |
| Gobiidae | Glossogobius obscuripinnis | native |
| Carcharhinidae | Glyphis gangeticus | Ganges shark | questionable |
| Gobiidae | Gnatholepis volcanus | native |
| Gobiidae | Gobiopterus brachypterus | Bia | native |
| Gobiidae | Gobiopterus lacustris | Lacustrine goby | Dulong | endemic |
| Gobiidae | Gobiopterus stellatus | endemic |
| Kraemeriidae | Gobitrichinotus radiocularis | native |
| Phallostethidae | Gulaphallus bikolanus | native |
| Phallostethidae | Gulaphallus eximius | native |
| Phallostethidae | Gulaphallus falcifer | native |
| Phallostethidae | Gulaphallus mirabilis | native |
| Muraenidae | Gymnothorax polyuranodon | Freshwater moray | native |
| Cyprinidae | Hampala lopezi | Manumbok | native |
| Helostomatidae | Helostoma temminkii | Kissing gourami | Kissing gourami | introduced |
| Gobiidae | Hemigobius hoevenii | Bia | native |
| Ariidae | Hemipimelodus manillensis | native |
| Syngnathidae | Hippichthys heptagonus | Belly pipefish | Dagum-dagum | native |
| Syngnathidae | Hippichthys penicillus | Beady pipefish | native |
| Siluridae | Hito taytayensis | Hito | endemic |
| Cyprinidae | Hypophthalmichthys molitrix | Silver carp | Babangan | not established |
| Hemiramphidae | Hyporhamphus quoyi | Quoy's garfish | Bugiw | native |
| Loricariidae | Hypostomus plecostomus | Suckermouth catfish | Plecostomus | introduced |
| Eleotridae | Hypseleotris agilis | Bagong lipunan | endemic |
| Eleotridae | Hypseleotris bipartita | Maringyan | endemic |
| Eleotridae | Hypseleotris cyprinoides | Tropical carp-gudgeon | native |
| Eleotridae | Hypseleotris everetti | native |
| Eleotridae | Hypseleotris pangel | native |
| Ictaluridae | Ictalurus punctatus | Channel catfish | Channel catfish | introduced |
| Sciaenidae | Johnius borneensis | Sharpnose hammer croaker | Alakaak | native |
| Kuhliidae | Kuhlia marginata | Dark-margined flagtail | Damagan | native |
| Kuhliidae | Kuhlia rupestris | Rock flagtail | Damagan | native |
| Cyprinidae | Labeo rohita | Rohu | Rohu | introduced |
| Ophichthidae | Lamnostoma mindora | native |
| Ophichthidae | Lamnostoma taylori | native |
| Leiognathidae | Leiognathus dussumieri | Dussumier's ponyfish | Sapsap | native |
| Leiognathidae | Leiognathus equulus | Common ponyfish | Sap-sap | native |
| Terapontidae | Leiopotherapon plumbeus | Bagaong | native |
| Centrarchidae | Lepomis cyanellus | Green sunfish | introduced |
| Centrarchidae | Lepomis macrochirus | Bluegill | Sunfish | introduced |
| Loricariidae | Liposarcus disjunctivus | Vermiculated sailfin catfish | introduced |
| Loricariidae | Liposarcus pardalis | Amazon sailfin catfish | introduced |
| Mugilidae | Liza macrolepis | Largescale mullet | Talilong | native |
| Mugilidae | Liza melinoptera | Otomebora mullet | Araran | native |
| Mugilidae | Liza parmata | Broad-mouthed mullet | Banak | native |
| Mugilidae | Liza subviridis | Greenback mullet | Aligasin | native |
| Mugilidae | Liza vaigiensis | Squaretail mullet | Bunti | native |
| Lutjanidae | Lutjanus argentimaculatus | Mangrove red snapper | Isu | native |
| Lutjanidae | Lutjanus ehrenbergii | Blackspot snapper | Maya-maya | native |
| Lutjanidae | Lutjanus fuscescens | Freshwater snapper | Aluman | native |
| Lutjanidae | Lutjanus maxweberi | Pygmy snapper | Aha-an | native |
| Cyprinidae | Mandibularca resinus | Bagañgan | endemic |
| Gobiidae | Mangarinus waterousi | Bia | native |
| Megalopidae | Megalops cyprinoides | Indo-Pacific tarpon | Buan buan | native |
| Blenniidae | Meiacanthus anema | Threadless blenny | native |
| Terapontidae | Mesopristes argenteus | Silver grunter | native |
| Terapontidae | Mesopristes cancellatus | Tapiroid grunter | Bagaong | native |
| Terapontidae | Mesopristes iravi | native |
| Syngnathidae | Microphis brachyurus brachyurus | Short-tailed pipefish | Dagum-dagum | native |
| Syngnathidae | Microphis jagorii | native |
| Syngnathidae | Microphis leiaspis | Barhead pipefish | Dagum-dagum | native |
| Syngnathidae | Microphis manadensis | Menado pipefish | native |
| Syngnathidae | Microphis mento | Dagum-dagum | native |
| Syngnathidae | Microphis pleurostictus | endemic |
| Syngnathidae | Microphis retzii | Ragged-tail pipefish | Dagum-dagum | native |
| Centrarchidae | Micropterus salmoides | Largemouth bass | introduced |
| Apogonidae | Mionorus bombonensis | native |
| Cobitidae | Misgurnus anguillicaudatus | Oriental weatherfish | Dojo | introduced |
| Gobiidae | Mistichthys luzonensis | Sinarapan | endemic |
| Monodactylidae | Monodactylus argenteus | Silver moony | Bayang | native |
| Synbranchidae | Monopterus albus | Swamp eel | native |
| Mugilidae | Mugil cephalus | Flathead mullet | Aguas | native |
| Gobiidae | Mugilogobius cagayanensis | endemic |
| Muraenesocidae | Muraenesox cinereus | Daggertooth pike conger | Ubod | native |
| Cyprinidae | Nematabramis alestes | native |
| Cyprinidae | Nematabramis everetti | questionable |
| Cyprinidae | Nematabramis verecundus | endemic |
| Phallostethidae | Neostethus bicornis | native |
| Phallostethidae | Neostethus borneensis | native |
| Phallostethidae | Neostethus ctenophorus | native |
| Phallostethidae | Neostethus robertsi | native |
| Phallostethidae | Neostethus thessa | native |
| Phallostethidae | Neostethus villadolidi | native |
| Tetrarogidae | Neovespicula depressifrons | Leaf goblinfish | native |
| Hemiramphidae | Nomorhamphus bakeri | native |
| Hemiramphidae | Nomorhamphus manifesta | native |
| Hemiramphidae | Nomorhamphus pectoralis | native |
| Hemiramphidae | Nomorhamphus philippina | endemic |
| Hemiramphidae | Nomorhamphus pinnimaculata | native |
| Hemiramphidae | Nomorhamphus rossi | native |
| Hemiramphidae | Nomorhamphus vivipara | native |
| Gobiidae | Oligolepis acutipennis | Sharptail goby | Bia | native |
| Blenniidae | Omobranchus ferox | Gossamer blenny | native |
| Eleotridae | Ophieleotris aporos | Snakehead gudgeon | Palawan | native |
| Eleotridae | Ophiocara porocephala | Northern mud gudgeon | Matapolo | native |
| Synbranchidae | Ophisternon bengalense | Bengal eel | Palos | native |
| Cichlidae | Oreochromis aureus | Blue tilapia | Tilapia | introduced |
| Cichlidae | Oreochromis mossambicus | Mozambique tilapia | introduced |
| Cichlidae | Oreochromis niloticus niloticus | Nile tilapia | Pla pla | introduced |
| Cichlidae | Oreochromis spilurus spilurus | Sabaki tilapia | introduced |
| Adrianichthyidae | Oryzias luzonensis | Coscosleng | native |
| Cyprinidae | Ospatulus palaemophagus | endemic |
| Cyprinidae | Ospatulus truncatulus | Bitungu | endemic |
| Osphronemidae | Osphronemus goramy | Giant gourami | Goramy | introduced |
| Eleotridae | Oxyeleotris expatria | Bulokot | endemic |
| Eleotridae | Oxyeleotris marmorata | Marble goby | Bia | native |
| Gobiidae | Pandaka pygmaea | Dwarf pygmy goby | Bia | native |
| Gobiidae | Pandaka trimaculata | Bia | native |
| Pangasiidae | Pangasius hypophthalmus | Sutchi catfish | introduced |
| Soleidae | Pardachirus poropterus | Estuary sole | native |
| Eleotridae | Parviparma straminea | native |
| Pristigasteridae | Pellona ditchela | Indian pellona | Dilat | native |
| Gobiidae | Periophthalmus argentilineatus | Barred mudskipper | Bia | native |
| Gobiidae | Periophthalmus malaccensis | Bia | native |
| Ophichthidae | Pisodonophis boro | Rice-paddy eel | Boro | native |
| Ophichthidae | Pisodonophis cancrivorus | Longfin snake-eel | native |
| Haemulidae | Plectorhinchus lineatus | Yellowbanded sweetlips | Labian | native |
| Poeciliidae | Poecilia latipinna | Sailfin molly | Bubuntis | introduced |
| Poeciliidae | Poecilia reticulata | Guppy | Guppy | introduced |
| Poeciliidae | Poecilia sphenops | Molly | Molly | introduced |
| Haemulidae | Pomadasys argenteus | Silver grunt | Bakoko | native |
| Pristidae | Pristis microdon | Largetooth sawfish | Barasan | native |
| Pristidae | Pristis pectinata | Smalltooth sawfish | native |
| Gobiidae | Pseudogobius javanicus | Bia | native |
| Gobiidae | Pseudogobius poicilosoma | Bia | native |
| Cyprinidae | Puntius amarus | Pait | endemic |
| Cyprinidae | Puntius bantolanensis | endemic |
| Cyprinidae | Puntius baoulan | Baoulan | endemic |
| Cyprinidae | Puntius binotatus | Spotted barb | Pait | native |
| Cyprinidae | Puntius cataractae | endemic |
| Cyprinidae | Puntius clemensi | Bagangan | endemic |
| Cyprinidae | Puntius disa | Disa | endemic |
| Cyprinidae | Puntius flavifuscus | Katapa-tapa | endemic |
| Cyprinidae | Puntius hemictenus | Pait | endemic |
| Cyprinidae | Puntius herrei | endemic |
| Cyprinidae | Puntius katolo | Katolo | endemic |
| Cyprinidae | Puntius lanaoensis | Kandar | endemic |
| Cyprinidae | Puntius lindog | Lindog | endemic |
| Cyprinidae | Puntius manalak | Manalak | endemic |
| Cyprinidae | Puntius manguaoensis | endemic |
| Cyprinidae | Puntius montanoi | endemic |
| Cyprinidae | Puntius pachycheilus | endemic |
| Cyprinidae | Puntius sirang | Sirang | endemic |
| Cyprinidae | Puntius tras | Tras | endemic |
| Cyprinidae | Puntius tumba | Tumba | endemic |
| Cyprinidae | Rasbora argyrotaenia | Silver rasbora | native |
| Cyprinidae | Rasbora borapetensis | Blackline rasbora | Red tail rasbora | native |
| Cyprinidae | Rasbora lateristriata | Yellow rasbora | native |
| Cyprinidae | Rasbora philippina | Mindanao rasbora | endemic |
| Cyprinidae | Rasbora punctulatus | endemic |
| Cyprinidae | Rasbora semilineata | native |
| Cyprinidae | Rasbora taytayensis | endemic |
| Gobiidae | Redigobius balteatus | Bia | native |
| Gobiidae | Redigobius bikolanus | Speckled goby | Bia | native |
| Gobiidae | Redigobius chrysosoma | Bia | native |
| Gobiidae | Redigobius dispar | Bia | native |
| Gobiidae | Redigobius roemeri | Roemer's goby | Bia | native |
| Gobiidae | Redigobius sapangus | Bia | native |
| Gobiidae | Redigobius tambujon | Bia | native |
| Gobiidae | Rhinogobius bucculentus | native |
| Gobiidae | Rhinogobius carpenteri | Kuchu | native |
| Gobiidae | Rhinogobius flavoventris | endemic |
| Rhyacichthyidae | Rhyacichthys aspro | Loach goby | Dalapakan | native |
| Hemiramphidae | Rhynchorhamphus georgii | Long billed half beak | Bugiw | native |
| Clupeidae | Sardinella tawilis | Freshwater sardinella | Tabagak | endemic |
| Scatophagidae | Scatophagus argus | Spotted scat | Kikiro | native |
| Gobiidae | Schismatogobius bruynisi | native |
| Gobiidae | Schismatogobius deraniyagalai | Redneck goby | native |
| Gobiidae | Schismatogobius marmoratus | native |
| Gobiidae | Schismatogobius pallidus | native |
| Gobiidae | Schismatogobius roxasi | native |
| Osteoglossidae | Scleropages formosus | Asian bonytongue | Golden arowana | native |
| Leiognathidae | Secutor ruconius | Deep pugnose ponyfish | Tambong bilog | native |
| Gobiidae | Sicyopterus crassus | native |
| Gobiidae | Sicyopterus cynocephalus | Cleft-lipped goby | native |
| Gobiidae | Sicyopterus fuliag | native |
| Gobiidae | Sicyopterus lacrymosus | Ipon | native |
| Gobiidae | Sicyopterus lagocephalus | Bichique | native |
| Gobiidae | Sicyopterus longifilis | Threadfin goby | native |
| Gobiidae | Sicyopterus macrostetholepis | native |
| Gobiidae | Sicyopterus micrurus | Clinging goby | native |
| Gobiidae | Sicyopterus panayensis | native |
| Gobiidae | Sicyopus auxilimentus | native |
| Gobiidae | Sicyopus cebuensis | native |
| Gobiidae | Sicyopus zosterophorum | native |
| Sillaginidae | Sillago macrolepis | Large-scale sillago | Asohos | native |
| Siluridae | Silurus palavanensis | endemic |
| Cyprinidae | Spratellicypris palata | Kandar | endemic |
| Gobiidae | Stenogobius genivittatus | Chinstripe goby | native |
| Gobiidae | Stenogobius kyphosus | native |
| Gobiidae | Stenogobius ophthalmoporus | Biyang tulis | native |
| Gobiidae | Stiphodon atropurpureus | native |
| Gobiidae | Stiphodon elegans | native |
| Gobiidae | Stiphodon olivaceus | native |
| Gobiidae | Stiphodon semoni | native |
| Gobiidae | Stiphodon surrufus | native |
| Belonidae | Strongylura strongylura | Spottail needlefish | Balo | native |
| Muraenidae | Strophidon sathete | Slender giant moray | Malibanos | native |
| Gobiidae | Taenioides anguillaris | Eel worm goby | native |
| Gobiidae | Taenioides gracilis | Slender eel goby | native |
| Gobiidae | Tamanka maculata | endemic |
| Gobiidae | Tamanka siitensis | endemic |
| Terapontidae | Terapon jarbua | Jarbua terapon | Kanigit | native |
| Tetraodontidae | Tetraodon nigroviridis | Spotted green pufferfish | native |
| Tetrarogidae | Tetraroge barbata | Bearded roguefish | native |
| Tetrarogidae | Tetraroge niger | native |
| Cichlidae | Tilapia zillii | Redbelly tilapia | Zill's tilapia | introduced |
| Toxotidae | Toxotes chatareus | Largescale archerfish | Ataba | native |
| Toxotidae | Toxotes jaculatrix | Banded archerfish | Ataba | native |
| Osphronemidae | Trichogaster leerii | Pearl gourami | Pearl gourami | introduced |
| Osphronemidae | Trichogaster pectoralis | Snakeskin gourami | Snakeskin gourami | introduced |
| Osphronemidae | Trichogaster trichopterus | Three spot gourami | Blue gourami | introduced |
| Gobiidae | Trypauchenichthys typus | native |
| Gobiidae | Tukugobius philippinus | Lizard goby | native |
| Mugilidae | Valamugil seheli | Bluespot mullet | Talilong | native |
| Ophichthidae | Yirrkala kaupii | native |
| Hemiramphidae | Zenarchopterus dispar | Feathered river-garfish | Kansusuit | native |
| Hemiramphidae | Zenarchopterus gilli | Viviparous halfbeak | native |
| Hemiramphidae | Zenarchopterus kampeni | Sepik River halfbeak | native |
| Hemiramphidae | Zenarchopterus philippinus | endemic |