| Family | Species | FishBase name | Threat Category | Occurrence |
|---|---|---|---|---|
| Cyprinidae | Cyclocheilichthys schoppeae | Endangered (EN) | endemic | |
| Zenarchopteridae | Dermogenys palawanensis | Vulnerable (VU) | endemic | |
| Blenniidae | Ecsenius kurti | Kurt's coralblenny | Vulnerable (VU) | endemic |
| Blenniidae | Ecsenius tricolor | Tricolor coralblenny | Vulnerable (VU) | native |
| Epinephelidae | Epinephelus bruneus | Longtooth grouper | Vulnerable (VU) | native |
| Epinephelidae | Epinephelus fuscoguttatus | Brown-marbled grouper | Vulnerable (VU) | native |
| Epinephelidae | Epinephelus polyphekadion | Camouflage grouper | Vulnerable (VU) | native |
| Sphyrnidae | Eusphyra blochii | Winghead shark | Endangered (EN) | native |
| Sparidae | Evynnis cardinalis | Threadfin porgy | Endangered (EN) | native |
| Gobiidae | Exyrias volcanus | Critically Endangered (CR) | endemic | |
| Glaucostegidae | Glaucostegus typus | Giant shovelnose ray | Critically Endangered (CR) | native |
| Gobiidae | Gobiodon aoyagii | Vulnerable (VU) | native | |
| Gobiidae | Gobiodon fulvus | Vulnerable (VU) | native | |
| Phallostethidae | Gulaphallus bikolanus | Endangered (EN) | endemic | |
| Phallostethidae | Gulaphallus eximius | Vulnerable (VU) | endemic | |
| Gymnuridae | Gymnura japonica | Japanese butterflyray | Vulnerable (VU) | native |
| Gymnuridae | Gymnura poecilura | Long-tailed butterfly ray | Vulnerable (VU) | native |
| Gymnuridae | Gymnura zonura | Zonetail butterfly ray | Endangered (EN) | native |
| Cyprinidae | Hampala lopezi | Endangered (EN) | native | |
| Hemigaleidae | Hemigaleus microstoma | Sicklefin weasel shark | Vulnerable (VU) | native |
| Hemigaleidae | Hemipristis elongata | Snaggletooth shark | Vulnerable (VU) | native |
| Triakidae | Hemitriakis leucoperiptera | Whitefin topeshark | Critically Endangered (CR) | endemic |
| Dasyatidae | Himantura leoparda | Vulnerable (VU) | native | |
| Dasyatidae | Himantura uarnak | Honeycomb stingray | Endangered (EN) | native |
| Syngnathidae | Hippocampus barbouri | Barbour's seahorse | Vulnerable (VU) | native |
| Syngnathidae | Hippocampus comes | Tiger tail seahorse | Vulnerable (VU) | native |
| Syngnathidae | Hippocampus histrix | Thorny seahorse | Vulnerable (VU) | native |
| Syngnathidae | Hippocampus kelloggi | Great seahorse | Vulnerable (VU) | native |
| Syngnathidae | Hippocampus kuda | Spotted seahorse | Vulnerable (VU) | native |
| Syngnathidae | Hippocampus spinosissimus | Hedgehog seahorse | Vulnerable (VU) | native |
| Syngnathidae | Hippocampus trimaculatus | Longnose seahorse | Vulnerable (VU) | native |
| Lamnidae | Isurus oxyrinchus | Shortfin mako | Endangered (EN) | native |
| Terapontidae | Leiopotherapon plumbeus | Vulnerable (VU) | endemic | |
| Dasyatidae | Maculabatis macrura | Endangered (EN) | native | |
| Syngnathidae | Microphis pleurostictus | Endangered (EN) | endemic | |
| Gobiidae | Mistichthys luzonensis | Sinarapan | Vulnerable (VU) | endemic |
| Mobulidae | Mobula alfredi | Alfred manta | Vulnerable (VU) | native |
| Mobulidae | Mobula birostris | Giant manta | Endangered (EN) | native |
| Mobulidae | Mobula eregoodootenkee | Longhorned mobula | Endangered (EN) | native |
| Mobulidae | Mobula kuhlii | Shortfin devil ray | Endangered (EN) | native |
| Mobulidae | Mobula mobular | Devil fish | Endangered (EN) | native |
| Mobulidae | Mobula tarapacana | Chilean devil ray | Endangered (EN) | native |
| Mobulidae | Mobula thurstoni | Smoothtail mobula | Endangered (EN) | native |
| Molidae | Mola mola | Ocean sunfish | Vulnerable (VU) | native |
| Gobiidae | Mugilogobius cagayanensis | Endangered (EN) | endemic | |
| Narcinidae | Narcine lingula | Chinese numbfish | Vulnerable (VU) | native |
| Narcinidae | Narcine maculata | Darkfinned numbfish | Vulnerable (VU) | native |
| Narcinidae | Narcine timlei | Spotted numbfish | Vulnerable (VU) | native |
| Ginglymostomatidae | Nebrius ferrugineus | Tawny nurse shark | Vulnerable (VU) | native |
| Carcharhinidae | Negaprion acutidens | Sicklefin lemon shark | Endangered (EN) | native |