| Order | Family | Species | Occurrence | FishBase name | Name |
|---|---|---|---|---|---|
| Perciformes | Cichlidae | Amatitlania nigrofasciata | introduced | Convict cichlid | Convict |
| Perciformes | Ambassidae | Ambassis buruensis | native | Buru glass perchlet | |
| Perciformes | Ambassidae | Ambassis gymnocephalus | native | Bald glassy | Langarai |
| Perciformes | Ambassidae | Ambassis interrupta | native | Long-spined glass perchlet | Langaray |
| Perciformes | Ambassidae | Ambassis macracanthus | native | Estuarine glass perchlet | |
| Perciformes | Ambassidae | Ambassis nalua | native | Scalloped perchlet | |
| Perciformes | Ambassidae | Ambassis urotaenia | native | Banded-tail glassy perchlet | |
| Perciformes | Anabantidae | Anabas testudineus | introduced | Climbing perch | Liwalo |
| Cypriniformes | Cyprinidae | Anematichthys armatus | native | ||
| Anguilliformes | Anguillidae | Anguilla australis | native | Short-finned eel | Igat |
| Anguilliformes | Anguillidae | Anguilla bengalensis | native | Indian mottled eel | Igat |
| Anguilliformes | Anguillidae | Anguilla bicolor | native | Indonesian shortfin eel | Igat |
| Anguilliformes | Anguillidae | Anguilla celebesensis | native | Celebes longfin eel | Igat |
| Anguilliformes | Anguillidae | Anguilla japonica | native | Japanese eel | Japanese eel |
| Anguilliformes | Anguillidae | Anguilla luzonensis | native | ||
| Anguilliformes | Anguillidae | Anguilla malgumora | native | Indonesian longfinned eel | |
| Anguilliformes | Anguillidae | Anguilla marmorata | native | Giant mottled eel | Igat |
| Rhinopristiformes | Pristidae | Anoxypristis cuspidata | native | Pointed sawfish | |
| Lophiiformes | Antennariidae | Antennarius biocellatus | native | Brackishwater frogfish | |
| Cyprinodontiformes | Aplocheilidae | Aplocheilus panchax | introduced | Blue panchax | Killie |
| Siluriformes | Ariidae | Arius dispar | native | Fleshysnout catfish | Kanduli |
| Siluriformes | Ariidae | Arius manillensis | endemic | Sea catfish | |
| Atheriniformes | Atherinidae | Atherinomorus duodecimalis | native | Tropical silverside | Gono |
| Atheriniformes | Atherinidae | Atherinomorus lacunosus | native | Wide-banded hardyhead silverside | Gono |
| Cyprinodontiformes | Rivulidae | Austrolebias nigripinnis | introduced | Blackfin pearlfish | |
| Perciformes | Gobiidae | Awaous grammepomus | native | Scribbled goby | Bia |
| Perciformes | Gobiidae | Awaous litturatus | endemic | ||
| Perciformes | Gobiidae | Awaous melanocephalus | native | Largesnout goby | Biang bato |
| Perciformes | Gobiidae | Awaous ocellaris | native | Bia | |
| Cypriniformes | Cyprinidae | Barbodes amarus | endemic | Dipura | |
| Cypriniformes | Cyprinidae | Barbodes bantolanensis | endemic | ||
| Cypriniformes | Cyprinidae | Barbodes baoulan | endemic | Baolan | |
| Cypriniformes | Cyprinidae | Barbodes binotatus | native | Spotted barb | Pait |
| Cypriniformes | Cyprinidae | Barbodes cataractae | endemic | ||
| Cypriniformes | Cyprinidae | Barbodes clemensi | endemic | Bagangan | |
| Cypriniformes | Cyprinidae | Barbodes disa | endemic | Disa | |
| Cypriniformes | Cyprinidae | Barbodes flavifuscus | endemic | Tumba | |
| Cypriniformes | Cyprinidae | Barbodes hemictenus | endemic | Pait | |
| Cypriniformes | Cyprinidae | Barbodes herrei | endemic | ||
| Cypriniformes | Cyprinidae | Barbodes ivis | native | ||
| Cypriniformes | Cyprinidae | Barbodes joaquinae | native | ||
| Cypriniformes | Cyprinidae | Barbodes katolo | endemic | Katolo | |
| Cypriniformes | Cyprinidae | Barbodes lanaoensis | endemic | Kandar | |
| Cypriniformes | Cyprinidae | Barbodes lindog | endemic | Lindog | |
| Cypriniformes | Cyprinidae | Barbodes manalak | endemic | Manalak | |
| Cypriniformes | Cyprinidae | Barbodes manguaoensis | endemic | ||
| Cypriniformes | Cyprinidae | Barbodes montanoi | endemic | ||
| Cypriniformes | Cyprinidae | Barbodes pachycheilus | endemic | ||
| Cypriniformes | Cyprinidae | Barbodes palaemophagus | endemic | Bitungu | |
| Cypriniformes | Cyprinidae | Barbodes palata | endemic | Kandar | |
| Cypriniformes | Cyprinidae | Barbodes palavanensis | native | ||
| Cypriniformes | Cyprinidae | Barbodes quinquemaculatus | native | ||
| Cypriniformes | Cyprinidae | Barbodes resinus | endemic | Bagañgan | |
| Cypriniformes | Cyprinidae | Barbodes sirang | endemic | Sirang | |
| Cypriniformes | Cyprinidae | Barbodes tras | endemic | Tras | |
| Cypriniformes | Cyprinidae | Barbodes truncatulus | endemic | Bitungu | |
| Cypriniformes | Cyprinidae | Barbodes tumba | endemic | Tumba | |
| Cypriniformes | Cyprinidae | Barbodes umalii | native | ||
| Cypriniformes | Cyprinidae | Barbonymus gonionotus | introduced | Silver barb | Tawes |
| Perciformes | Gobiidae | Bathygobius fuscus | native | Dusky frillgoby | Bia |
| Perciformes | Eleotridae | Belobranchus belobranchus | native | Throat-spine gudgeon | Batingulo |
| Perciformes | Gobiidae | Boleophthalmus boddarti | native | Boddart's goggle-eyed goby | Bia |
| Perciformes | Eleotridae | Bostrychus albooculata | native | ||
| Perciformes | Eleotridae | Bostrychus expatria | endemic | Bulokot | |
| Perciformes | Gobiidae | Brachygobius aggregatus | native | Schooling bumblebee goby | Bia |
| Perciformes | Eleotridae | Bunaka gyrinoides | native | Greenback gauvina | Boto-bot |
| Perciformes | Eleotridae | Butis amboinensis | native | Olive flathead-gudgeon | Biyang sunog |
| Perciformes | Eleotridae | Butis butis | native | Duckbill sleeper | Pasel |
| Perciformes | Eleotridae | Butis gymnopomus | native | ||
| Perciformes | Eleotridae | Butis koilomatodon | native | Mud sleeper | |
| Perciformes | Gobiidae | Caecogobius cryptophthalmus | endemic | ||
| Perciformes | Gobiidae | Callogobius hasseltii | native | Hasselt's goby | Bia |
| Perciformes | Gobiidae | Caragobius urolepis | native | Scaleless worm goby | Bia |
| Cypriniformes | Cyprinidae | Carassius auratus | introduced | Goldfish | karpita |
| Cypriniformes | Cyprinidae | Carassius carassius | introduced | Crucian carp | Wild goldfish |
| Carcharhiniformes | Carcharhinidae | Carcharhinus leucas | native | Bull shark | Pating |
| Siluriformes | Ariidae | Cephalocassis manillensis | endemic | ||
| Mugiliformes | Mugilidae | Cestraeus goldiei | native | Goldie river mullet | Banak |
| Mugiliformes | Mugilidae | Cestraeus oxyrhyncus | native | Sharp-nosed river mullet | Banak |
| Mugiliformes | Mugilidae | Cestraeus plicatilis | native | Lobed river mullet | Ludong |
| Perciformes | Channidae | Channa maculata | native | Blotched snakehead | |
| Perciformes | Channidae | Channa melasoma | native | Black snakehead | |
| Perciformes | Channidae | Channa striata | introduced | Striped snakehead | Anak dalag |
| Gonorynchiformes | Chanidae | Chanos chanos | native | Milkfish | Awa |
| Mugiliformes | Mugilidae | Chelon macrolepis | native | Largescale mullet | Talilong |
| Mugiliformes | Mugilidae | Chelon melinopterus | native | Otomebora mullet | Araran |
| Mugiliformes | Mugilidae | Chelon subviridis | native | Greenback mullet | Aligasin |
| Osteoglossiformes | Notopteridae | Chitala chitala | introduced | Clown knifefish | |
| Osteoglossiformes | Notopteridae | Chitala ornata | introduced | Clown featherback | |
| Cypriniformes | Cyprinidae | Cirrhinus cirrhosus | introduced | Mrigal carp | |
| Siluriformes | Clariidae | Clarias batrachus | introduced | Philippine catfish | Hitong batukan |
| Siluriformes | Clariidae | Clarias fuscus | native | Hong Kong catfish | |
| Siluriformes | Clariidae | Clarias gariepinus | introduced | North African catfish | |
| Siluriformes | Clariidae | Clarias macrocephalus | native | Bighead catfish | Hito |
| Siluriformes | Clariidae | Clarias meladerma | native | Blackskin catfish | |
| Siluriformes | Clariidae | Clarias nieuhofii | native | Slender walking catfish | |
| Clupeiformes | Clupeidae | Clupea manulensis | native | ||
| Characiformes | Serrasalmidae | Colossoma macropomum | introduced | Cachama | |
| Perciformes | Cichlidae | Coptodon zillii | introduced | Redbelly tilapia | Zill's tilapia |
| Siluriformes | Callichthyidae | Corydoras aeneus | introduced | Bronze corydoras | Bronze catfish |
| Mugiliformes | Mugilidae | Crenimugil heterocheilos | native | Half fringelip mullet | Banak |
| Cypriniformes | Cyprinidae | Cyclocheilichthys schoppeae | endemic | ||
| Pleuronectiformes | Cynoglossidae | Cynoglossus puncticeps | native | Speckled tonguesole | Ararali |
| Cypriniformes | Cyprinidae | Cyprinus carpio | introduced | Common carp | Karpa |
| Cypriniformes | Cyprinidae | Danio rerio | introduced | Zebra danio | Zebra danio |
| Beloniformes | Zenarchopteridae | Dermogenys palawanensis | endemic | ||
| Beloniformes | Zenarchopteridae | Dermogenys robertsi | endemic | ||
| Tetraodontiformes | Tetraodontidae | Dichotomyctere nigroviridis | native | Spotted green pufferfish | |
| Syngnathiformes | Syngnathidae | Doryichthys boaja | native | ||
| Syngnathiformes | Syngnathidae | Doryichthys martensii | native | ||
| Clupeiformes | Dussumieriidae | Dussumieria acuta | native | Rainbow sardine | Balantiong |
| Anguilliformes | Muraenidae | Echidna leucotaenia | native | Whiteface moray | |
| Anguilliformes | Muraenidae | Echidna rhodochilus | native | Pink-lipped moray eel | |
| Perciformes | Eleotridae | Eleotris acanthopoma | native | Spinecheek gudgeon | |
| Perciformes | Eleotridae | Eleotris fusca | native | Dusky sleeper | Batingulo |
| Perciformes | Eleotridae | Eleotris mauritiana | native | Widehead sleeper | |
| Perciformes | Eleotridae | Eleotris melanosoma | native | Broadhead sleeper | Ipon |
| Perciformes | Polynemidae | Eleutheronema tetradactylum | native | Fourfinger threadfin | Mamale |
| Mugiliformes | Mugilidae | Ellochelon vaigiensis | native | Squaretail mullet | Bunti |
| Elopiformes | Elopidae | Elops hawaiensis | native | Hawaiian ladyfish | Bid-bid |
| Perciformes | Serranidae | Epinephelus polystigma | native | White-dotted grouper | Lapu lapu |
| Perciformes | Gobiidae | Eugnathogobius illotus | native | ||
| Perciformes | Gobiidae | Exyrias volcanus | endemic | Goby | |
| Perciformes | Gobiidae | Favonigobius reichei | native | Indo-Pacific tropical sand goby | Bia |
| Cyprinodontiformes | Fundulidae | Fundulus heteroclitus | introduced | Mummichog | |
| Cyprinodontiformes | Poeciliidae | Gambusia affinis | introduced | Mosquitofish | Isdang canal |
| Perciformes | Gerreidae | Gerres filamentosus | native | Whipfin silver-biddy | Batuhanon |
| Cypriniformes | Cyprinidae | Gibelion catla | introduced | Catla | |
| Perciformes | Eleotridae | Giuris margaritacea | native | Snakehead gudgeon | Buguwan |
| Perciformes | Gobiidae | Glossogobius aureus | native | Golden tank goby | Bia |
| Perciformes | Gobiidae | Glossogobius bicirrhosus | native | Bearded flathead goby | Bia |
| Perciformes | Gobiidae | Glossogobius celebius | native | Celebes goby | Biyang bato |
| Perciformes | Gobiidae | Glossogobius circumspectus | native | Circumspect goby | Bia |
| Perciformes | Gobiidae | Glossogobius clitellus | native | ||
| Perciformes | Gobiidae | Glossogobius giuris | native | Tank goby | Bia |
| Perciformes | Gobiidae | Glossogobius obscuripinnis | native | ||
| Perciformes | Gobiidae | Gobiopterus brachypterus | native | Bia | |
| Perciformes | Gobiidae | Gobiopterus lacustris | endemic | Lacustrine goby | Dulong |
| Perciformes | Gobiidae | Gobiopterus stellatus | endemic | Dwarf freshwater goby | Dolong |
| Perciformes | Kraemeriidae | Gobitrichinotus radiocularis | native | ||
| Atheriniformes | Phallostethidae | Gulaphallus bikolanus | endemic | ||
| Atheriniformes | Phallostethidae | Gulaphallus eximius | endemic | ||
| Atheriniformes | Phallostethidae | Gulaphallus falcifer | endemic | ||
| Atheriniformes | Phallostethidae | Gulaphallus mirabilis | endemic | ||
| Anguilliformes | Muraenidae | Gymnothorax meleagris | native | Turkey moray | Malibanos |
| Anguilliformes | Muraenidae | Gymnothorax polyuranodon | native | Freshwater moray | |
| Cypriniformes | Cyprinidae | Hampala lopezi | native | Manumbok | |
| Perciformes | Helostomatidae | Helostoma temminkii | introduced | Kissing gourami | Kissing gourami |
| Perciformes | Gobiidae | Hemigobius hoevenii | native | Banded mulletgoby | Bia |
| Clupeiformes | Clupeidae | Herklotsichthys quadrimaculatus | native | Bluestripe herring | Tunsoy |
| Syngnathiformes | Syngnathidae | Hippichthys heptagonus | native | Belly pipefish | Dagum-dagum |
| Syngnathiformes | Syngnathidae | Hippichthys penicillus | native | Beady pipefish | |
| Cypriniformes | Cyprinidae | Hypophthalmichthys molitrix | introduced | Silver carp | Babangan |
| Cypriniformes | Cyprinidae | Hypophthalmichthys nobilis | introduced | Bighead carp | |
| Beloniformes | Hemiramphidae | Hyporhamphus quoyi | native | Quoy's garfish | Bugiw |
| Siluriformes | Loricariidae | Hypostomus plecostomus | introduced | Suckermouth catfish | Plecostomus |
| Perciformes | Eleotridae | Hypseleotris cyprinoides | native | Tropical carp-gudgeon | Maringyan |
| Perciformes | Eleotridae | Hypseleotris everetti | endemic | ||
| Perciformes | Eleotridae | Hypseleotris pangel | endemic | ||
| Siluriformes | Ictaluridae | Ictalurus punctatus | introduced | Channel catfish | Channel catfish |
| Perciformes | Sciaenidae | Johnius borneensis | native | Sharpnose hammer croaker | Alakaak |
| Perciformes | Kuhliidae | Kuhlia marginata | native | Dark-margined flagtail | Damagan |
| Perciformes | Kuhliidae | Kuhlia rupestris | native | Rock flagtail | Damagan |
| Cypriniformes | Cyprinidae | Labeo rohita | introduced | Roho labeo | Rohu |
| Cypriniformes | Cyprinidae | Labiobarbus cyanopareja | native | ||
| Anguilliformes | Ophichthidae | Lamnostoma kampeni | native | Freshwater snake-eel | |
| Anguilliformes | Ophichthidae | Lamnostoma mindora | native | ||
| Anguilliformes | Ophichthidae | Lamnostoma orientalis | native | Oriental worm-eel | |
| Anguilliformes | Ophichthidae | Lamnostoma taylori | endemic | ||
| Perciformes | Latidae | Lates calcarifer | native | Barramundi | Apaap |
| Perciformes | Leiognathidae | Leiognathus equulus | native | Common ponyfish | Mawalay |
| Perciformes | Terapontidae | Leiopotherapon plumbeus | endemic | Silver perch | |
| Perciformes | Gobiidae | Lentipes mindanaoensis | native | ||
| Perciformes | Centrarchidae | Lepomis cyanellus | introduced | Green sunfish | |
| Perciformes | Centrarchidae | Lepomis macrochirus | introduced | Bluegill | Sunfish |
| Mugiliformes | Mugilidae | Liza alata | native | Diamond mullet | |
| Mugiliformes | Mugilidae | Liza argentea | native | Flat-tail mullet | Balanak |
| Perciformes | Lutjanidae | Lutjanus argentimaculatus | native | Mangrove red snapper | Gingaw |
| Perciformes | Lutjanidae | Lutjanus bohar | native | Two-spot red snapper | Langisi |
| Perciformes | Lutjanidae | Lutjanus ehrenbergii | native | Blackspot snapper | Alsis |
| Perciformes | Lutjanidae | Lutjanus fuscescens | native | Freshwater snapper | Aluman |
| Perciformes | Lutjanidae | Lutjanus johnii | native | John's snapper | Maya maya |
| Perciformes | Lutjanidae | Lutjanus malabaricus | native | Malabar blood snapper | Lugho |
| Perciformes | Lutjanidae | Lutjanus maxweberi | native | Pygmy snapper | Aha-an |
| Perciformes | Lutjanidae | Lutjanus monostigma | native | One-spot snapper | Maya maya |
| Perciformes | Gobiidae | Mangarinus waterousi | native | Bia | |
| Perciformes | Cichlidae | Mayaheros urophthalmus | introduced | Mexican mojarra | |
| Elopiformes | Megalopidae | Megalops cyprinoides | native | Indo-Pacific tarpon | Abulong |
| Perciformes | Blenniidae | Meiacanthus anema | native | Threadless blenny | |
| Perciformes | Terapontidae | Mesopristes argenteus | native | Silver grunter | |
| Perciformes | Terapontidae | Mesopristes cancellatus | native | Tapiroid grunter | Bagaong |
| Perciformes | Terapontidae | Mesopristes iravi | native | ||
| Syngnathiformes | Syngnathidae | Microphis brachyurus | native | Short-tailed pipefish | Dagum-dagum |
| Syngnathiformes | Syngnathidae | Microphis leiaspis | native | Barhead pipefish | Dagum-dagum |
| Syngnathiformes | Syngnathidae | Microphis manadensis | native | Menado pipefish | |
| Syngnathiformes | Syngnathidae | Microphis mento | native | Dagum-dagum | |
| Syngnathiformes | Syngnathidae | Microphis pleurostictus | endemic | ||
| Syngnathiformes | Syngnathidae | Microphis retzii | native | Ragged-tail pipefish | Dagum-dagum |
| Perciformes | Centrarchidae | Micropterus salmoides | introduced | Largemouth black bass | |
| Cypriniformes | Cobitidae | Misgurnus anguillicaudatus | introduced | Pond loach | Dojo |
| Perciformes | Gobiidae | Mistichthys luzonensis | endemic | Sinarapan | |
| Perciformes | Monodactylidae | Monodactylus argenteus | native | Silver moony | Bayang |
| Synbranchiformes | Synbranchidae | Monopterus albus | native | Asian swamp eel | |
| Mugiliformes | Mugilidae | Moolgarda cunnesius | native | Longarm mullet | Talilong |
| Mugiliformes | Mugilidae | Moolgarda seheli | native | Bluespot mullet | Talilong |
| Mugiliformes | Mugilidae | Mugil cephalus | native | Flathead grey mullet | Aguas |
| Perciformes | Gobiidae | Mugilogobius cagayanensis | endemic | ||
| Perciformes | Gobiidae | Mugilogobius mertoni | native | Chequered mangrove goby | |
| Anguilliformes | Muraenesocidae | Muraenesox cinereus | native | Daggertooth pike conger | Ubod |
| Cypriniformes | Cyprinidae | Nematabramis alestes | native | ||
| Cypriniformes | Cyprinidae | Nematabramis verecundus | endemic | ||
| Siluriformes | Ariidae | Neoarius leptaspis | native | Salmon catfish | |
| Atheriniformes | Phallostethidae | Neostethus bicornis | native | ||
| Atheriniformes | Phallostethidae | Neostethus borneensis | native | ||
| Atheriniformes | Phallostethidae | Neostethus ctenophorus | endemic | ||
| Atheriniformes | Phallostethidae | Neostethus robertsi | endemic | ||
| Atheriniformes | Phallostethidae | Neostethus thessa | endemic | Priapium fish | |
| Atheriniformes | Phallostethidae | Neostethus villadolidi | endemic | ||
| Scorpaeniformes | Tetrarogidae | Neovespicula depressifrons | native | Leaf goblinfish | |
| Beloniformes | Zenarchopteridae | Nomorhamphus bakeri | endemic | ||
| Beloniformes | Zenarchopteridae | Nomorhamphus manifesta | endemic | ||
| Beloniformes | Zenarchopteridae | Nomorhamphus pectoralis | endemic | ||
| Beloniformes | Zenarchopteridae | Nomorhamphus philippinus | endemic | ||
| Beloniformes | Zenarchopteridae | Nomorhamphus pinnimaculata | endemic | ||
| Beloniformes | Zenarchopteridae | Nomorhamphus rossi | endemic | ||
| Beloniformes | Zenarchopteridae | Nomorhamphus vivipara | endemic | ||
| Perciformes | Gobiidae | Oligolepis acutipennis | native | Sharptail goby | Bia |
| Perciformes | Gobiidae | Oligolepis keiensis | native | Kei goby | |
| Perciformes | Blenniidae | Omobranchus ferox | native | Gossamer blenny | |
| Syngnathiformes | Syngnathidae | Oostethus jagorii | native | ||
| Perciformes | Eleotridae | Ophiocara porocephala | native | Northern mud gudgeon | Matapolo |
| Synbranchiformes | Synbranchidae | Ophisternon bengalense | native | Bengal eel | Palos |
| Perciformes | Cichlidae | Oreochromis aureus | introduced | Blue tilapia | Tilapia |
| Perciformes | Cichlidae | Oreochromis mossambicus | introduced | Mozambique tilapia | Tilapia |
| Perciformes | Cichlidae | Oreochromis niloticus | introduced | Nile tilapia | Pla pla |
| Perciformes | Cichlidae | Oreochromis spilurus | introduced | Sabaki tilapia | |
| Beloniformes | Adrianichthyidae | Oryzias luzonensis | endemic | Coscosleng | |
| Perciformes | Osphronemidae | Osphronemus goramy | introduced | Giant gourami | Goramy |
| Perciformes | Eleotridae | Oxyeleotris marmorata | native | Marble goby | Bia |
| Perciformes | Gobiidae | Oxyurichthys ophthalmonema | native | Eyebrow goby | Bia |
| Perciformes | Gobiidae | Pandaka pygmaea | native | Dwarf pygmy goby | Bia |
| Perciformes | Gobiidae | Pandaka trimaculata | native | Bia | |
| Siluriformes | Pangasiidae | Pangasianodon hypophthalmus | introduced | Striped catfish | |
| Perciformes | Cichlidae | Parachromis managuensis | introduced | Jaguar guapote | Managuense |
| Mugiliformes | Mugilidae | Paramugil parmatus | native | Broad-mouthed mullet | Banak |
| Pleuronectiformes | Soleidae | Pardachirus poropterus | native | Estuary sole | |
| Clupeiformes | Pristigasteridae | Pellona ditchela | native | Indian pellona | Dilat |
| Perciformes | Gobiidae | Periophthalmus argentilineatus | native | Barred mudskipper | Bia |
| Perciformes | Gobiidae | Periophthalmus barbarus | native | Atlantic mudskipper | |
| Perciformes | Gobiidae | Periophthalmus malaccensis | native | Bia | |
| Anguilliformes | Ophichthidae | Pisodonophis boro | native | Rice-paddy eel | Boro |
| Anguilliformes | Ophichthidae | Pisodonophis cancrivorus | native | Longfin snake-eel | |
| Siluriformes | Ariidae | Plicofollis magatensis | endemic | ||
| Cyprinodontiformes | Poeciliidae | Poecilia latipinna | introduced | Sailfin molly | Bubuntis |
| Cyprinodontiformes | Poeciliidae | Poecilia reticulata | introduced | Guppy | Guppy |
| Cyprinodontiformes | Poeciliidae | Poecilia sphenops | introduced | Molly | Molly |
| Perciformes | Pomacentridae | Pomacentrus tripunctatus | native | Threespot damsel | Puyong dagat |
| Perciformes | Haemulidae | Pomadasys argenteus | native | Silver grunt | Bakoko |
| Rhinopristiformes | Pristidae | Pristis microdon | native | Largetooth sawfish | Barasan |
| Perciformes | Gobiidae | Psammogobius biocellatus | native | Sleepy goby | Biyang tulog |
| Perciformes | Gobiidae | Pseudogobiopsis oligactis | native | ||
| Perciformes | Gobiidae | Pseudogobius javanicus | native | Goby of streams | |
| Perciformes | Gobiidae | Pseudogobius poicilosoma | native | Northern fatnose goby | Bia |
| Siluriformes | Siluridae | Pterocryptis taytayensis | endemic | Hito | |
| Siluriformes | Loricariidae | Pterygoplichthys disjunctivus | introduced | Vermiculated sailfin catfish | |
| Siluriformes | Loricariidae | Pterygoplichthys pardalis | introduced | Amazon sailfin catfish | |
| Cypriniformes | Cyprinidae | Puntigrus tetrazona | introduced | Sumatra barb | Tiger barb |
| Cypriniformes | Cyprinidae | Rasbora argyrotaenia | native | Silver rasbora | |
| Cypriniformes | Cyprinidae | Rasbora borapetensis | native | Blackline rasbora | Red tail rasbora |
| Cypriniformes | Cyprinidae | Rasbora everetti | native | ||
| Cypriniformes | Cyprinidae | Rasbora lateristriata | native | Yellow rasbora | |
| Cypriniformes | Cyprinidae | Rasbora philippina | endemic | Mindanao rasbora | |
| Cypriniformes | Cyprinidae | Rasbora semilineata | native | ||
| Cypriniformes | Cyprinidae | Rasbora taytayensis | endemic | ||
| Perciformes | Gobiidae | Redigobius balteatus | native | Rhinohorn goby | Bia |
| Perciformes | Gobiidae | Redigobius bikolanus | native | Speckled goby | Bia |
| Perciformes | Gobiidae | Redigobius chrysosoma | native | Bia | |
| Perciformes | Gobiidae | Redigobius dispar | native | Bia | |
| Perciformes | Gobiidae | Redigobius oyensi | native | ||
| Perciformes | Gobiidae | Redigobius tambujon | native | Goby of streams | |
| Perciformes | Gobiidae | Rhinogobius bucculentus | endemic | ||
| Perciformes | Gobiidae | Rhinogobius carpenteri | endemic | Kuchu | |
| Perciformes | Gobiidae | Rhinogobius flavoventris | endemic | Goby | |
| Perciformes | Gobiidae | Rhinogobius philippinus | endemic | Lizard goby | |
| Perciformes | Rhyacichthyidae | Rhyacichthys aspro | native | Loach goby | Dalapakan |
| Beloniformes | Hemiramphidae | Rhynchorhamphus georgii | native | Long billed half beak | Bugiw |
| Clupeiformes | Clupeidae | Sardinella tawilis | endemic | Freshwater sardinella | Hawo hawo |
| Perciformes | Cichlidae | Sarotherodon melanotheron | introduced | Blackchin tilapia | |
| Perciformes | Scatophagidae | Scatophagus argus | native | Spotted scat | Kero kero |
| Perciformes | Gobiidae | Schismatogobius bruynisi | native | ||
| Perciformes | Gobiidae | Schismatogobius deraniyagalai | native | Redneck goby | |
| Perciformes | Gobiidae | Schismatogobius marmoratus | native | ||
| Perciformes | Gobiidae | Schismatogobius pallidus | endemic | ||
| Perciformes | Gobiidae | Schismatogobius roxasi | native | ||
| Osteoglossiformes | Osteoglossidae | Scleropages formosus | introduced | Asian bonytongue | Golden arowana |
| Perciformes | Leiognathidae | Secutor ruconius | native | Deep pugnose ponyfish | Tambong bilog |
| Perciformes | Gobiidae | Sicyopterus crassus | endemic | ||
| Perciformes | Gobiidae | Sicyopterus cynocephalus | native | Cleft-lipped goby | |
| Perciformes | Gobiidae | Sicyopterus fuliag | endemic | ||
| Perciformes | Gobiidae | Sicyopterus lacrymosus | endemic | Ipon | |
| Perciformes | Gobiidae | Sicyopterus lagocephalus | native | Red-tailed goby | Anga |
| Perciformes | Gobiidae | Sicyopterus longifilis | native | Threadfin goby | |
| Perciformes | Gobiidae | Sicyopterus macrostetholepis | native | ||
| Perciformes | Gobiidae | Sicyopterus micrurus | native | Clinging goby | |
| Perciformes | Gobiidae | Sicyopterus panayensis | endemic | ||
| Perciformes | Gobiidae | Sicyopus auxilimentus | endemic | ||
| Perciformes | Gobiidae | Sicyopus cebuensis | endemic | ||
| Perciformes | Gobiidae | Sicyopus zosterophorus | native | ||
| Perciformes | Sillaginidae | Sillaginops macrolepis | native | Large-scale sillago | Asohos |
| Perciformes | Sillaginidae | Sillago sihama | native | Silver sillago | Aso-os |
| Perciformes | Gobiidae | Stenogobius genivittatus | native | Chinstripe goby | |
| Perciformes | Gobiidae | Stenogobius kyphosus | endemic | ||
| Perciformes | Gobiidae | Stenogobius laterisquamatus | native | ||
| Perciformes | Gobiidae | Stenogobius ophthalmoporus | native | Biyang tulis | |
| Perciformes | Gobiidae | Stigmatogobius elegans | endemic | ||
| Perciformes | Gobiidae | Stiphodon atropurpureus | native | ||
| Perciformes | Gobiidae | Stiphodon elegans | native | ||
| Perciformes | Gobiidae | Stiphodon palawanensis | native | ||
| Perciformes | Gobiidae | Stiphodon pulchellus | endemic | ||
| Perciformes | Gobiidae | Stiphodon semoni | native | ||
| Perciformes | Gobiidae | Stiphodon surrufus | endemic | ||
| Anguilliformes | Muraenidae | Strophidon sathete | native | Slender giant moray | Malibanos |
| Perciformes | Gobiidae | Taenioides anguillaris | native | Eel worm goby | |
| Perciformes | Gobiidae | Taenioides cirratus | native | Bearded worm goby | Baliga |
| Perciformes | Gobiidae | Taenioides gracilis | native | Slender eel goby | |
| Perciformes | Gobiidae | Tamanka maculata | endemic | ||
| Perciformes | Gobiidae | Tamanka siitensis | endemic | ||
| Perciformes | Terapontidae | Terapon jarbua | native | Jarbua terapon | Kanigit |
| Scorpaeniformes | Tetrarogidae | Tetraroge barbata | native | Bearded roguefish | |
| Scorpaeniformes | Tetrarogidae | Tetraroge niger | native | ||
| Perciformes | Toxotidae | Toxotes chatareus | native | Spotted archerfish | Ataba |
| Perciformes | Toxotidae | Toxotes jaculatrix | native | Banded archerfish | Ataba |
| Perciformes | Osphronemidae | Trichopodus leerii | introduced | Pearl gourami | Pearl gourami |
| Perciformes | Osphronemidae | Trichopodus pectoralis | introduced | Snakeskin gourami | Pla-salit |
| Perciformes | Osphronemidae | Trichopodus trichopterus | introduced | Three spot gourami | Pla-salit |
| Perciformes | Gobiidae | Trypauchenichthys typus | native | Typical eelgoby | |
| Beloniformes | Belonidae | Tylosurus acus melanotus | native | Keel-jawed needle fish | Balo |
| Perciformes | Apogonidae | Yarica hyalosoma | native | Humpbacked cardinalfish | Dangat |
| Anguilliformes | Ophichthidae | Yirrkala kaupii | native | ||
| Perciformes | Gobiidae | Yongeichthys criniger | native | Horny goby | |
| Beloniformes | Zenarchopteridae | Zenarchopterus dispar | native | Feathered river-garfish | Kansusuit |
| Beloniformes | Zenarchopteridae | Zenarchopterus gilli | native | Viviparous halfbeak | |
| Beloniformes | Zenarchopteridae | Zenarchopterus kampeni | native | Sepik River halfbeak | |
| Beloniformes | Zenarchopteridae | Zenarchopterus philippinus | endemic |