| Order | Family | Species | Status | FB name | Name |
| Perciformes | Ambassidae | Ambassis buruensis | native | Buru glass perchlet | |
| Perciformes | Ambassidae | Ambassis dussumieri | native | Malabar glassy perchlet | |
| Perciformes | Ambassidae | Ambassis macracanthus | native | Estuarine glass perchlet | |
| Perciformes | Ambassidae | Ambassis miops | native | Flag-tailed glass perchlet | |
| Perciformes | Ambassidae | Ambassis urotaenia | native | Banded-tail glassy perchlet | |
| Perciformes | Anabantidae | Anabas testudineus | native | Climbing perch | |
| Anguilliformes | Anguillidae | Anguilla bicolor bicolor | native | Indonesian shortfin eel | |
| Anguilliformes | Anguillidae | Anguilla celebesensis | native | Celebes longfin eel | |
| Anguilliformes | Anguillidae | Anguilla marmorata | native | Giant mottled eel | |
| Cyprinodontiformes | Aplocheilidae | Aplocheilus panchax | introduced | Blue panchax | |
| Atheriniformes | Atherinidae | Atherinomorus lacunosus | native | Hardyhead silverside | |
| Perciformes | Gobiidae | Awaous melanocephalus | native | Largesnout goby | |
| Perciformes | Eleotridae | Belobranchus belobranchus | native | Throat-spine gudgeon | |
| Perciformes | Eleotridae | Bunaka gyrinoides | native | Greenback gauvina | |
| Mugiliformes | Mugilidae | Cestraeus goldiei | native | Goldie river mullet | |
| Siluriformes | Clariidae | Clarias gariepinus | introduced | North African catfish | |
| Atheriniformes | Atherinidae | Craterocephalus laisapi | native | ||
| Cypriniformes | Cyprinidae | Cyprinus carpio carpio | introduced | Common carp | |
| Perciformes | Eleotridae | Eleotris fusca | native | Dusky sleeper | |
| Perciformes | Eleotridae | Eleotris margaritacea | native | ||
| Perciformes | Eleotridae | Eleotris melanosoma | native | Broadhead sleeper | |
| Cyprinodontiformes | Poeciliidae | Gambusia affinis | introduced | Mosquitofish | |
| Perciformes | Gerreidae | Gerres filamentosus | native | Whipfin silverbiddy | |
| Perciformes | Gobiidae | Glossogobius celebius | native | Celebes goby | |
| Perciformes | Kuhliidae | Kuhlia marginata | native | Dark-margined flagtail | |
| Perciformes | Kuhliidae | Kuhlia rupestris | native | Rock flagtail | |
| Perciformes | Latidae | Lates calcarifer | native | Barramundi | |
| Mugiliformes | Mugilidae | Liza subviridis | native | Greenback mullet | |
| Perciformes | Lutjanidae | Lutjanus fuscescens | native | Freshwater snapper | |
| Elopiformes | Megalopidae | Megalops cyprinoides | native | Indo-Pacific tarpon | |
| Perciformes | Terapontidae | Mesopristes argenteus | native | Silver grunter | |
| Perciformes | Terapontidae | Mesopristes cancellatus | native | Tapiroid grunter | |
| Syngnathiformes | Syngnathidae | Microphis retzii | native | Ragged-tail pipefish | |
| Perciformes | Gobiidae | Mugilogobius cavifrons | native | ||
| Perciformes | Eleotridae | Ophiocara porocephala | native | Northern mud gudgeon | |
| Perciformes | Cichlidae | Oreochromis mossambicus | native | Mozambique tilapia | |
| Beloniformes | Adrianichthyidae | Oryzias celebensis | native | Celebes medaka | |
| Beloniformes | Adrianichthyidae | Oryzias timorensis | endemic | ||
| Perciformes | Gobiidae | Periophthalmus argentilineatus | native | Barred mudskipper | |
| Cyprinodontiformes | Poeciliidae | Poecilia reticulata | native | Guppy | |
| Perciformes | Gobiidae | Pseudapocryptes borneensis | native | ||
| Perciformes | Scatophagidae | Scatophagus argus | native | Spotted scat | |
| Perciformes | Gobiidae | Sicyopterus cynocephalus | native | Cleft-lipped goby | |
| Perciformes | Gobiidae | Sicyopterus hageni | native | Hagen's goby | |
| Perciformes | Gobiidae | Sicyopterus wichmanni | native | ||
| Perciformes | Sillaginidae | Sillago sihama | native | Silver sillago | |
| Perciformes | Terapontidae | Terapon jarbua | native | Jarbua terapon | |
| Perciformes | Toxotidae | Toxotes jaculatrix | native | Banded archerfish |