| Family | Species | FishBase name | Threat Category | Occurrence |
|---|---|---|---|---|
| Centrophoridae | Centrophorus squamosus | Leafscale gulper shark | Endangered (EN) | native |
| Ariidae | Cephalocassis manillensis | Endangered (EN) | endemic | |
| Scyliorhinidae | Cephaloscyllium fasciatum | Reticulated swellshark | Critically Endangered (CR) | questionable |
| Cetorhinidae | Cetorhinus maximus | Basking shark | Endangered (EN) | questionable |
| Labridae | Cheilinus undulatus | Humphead wrasse | Endangered (EN) | native |
| Hemiscylliidae | Chiloscyllium indicum | Slender bambooshark | Vulnerable (VU) | questionable |
| Chimaeridae | Chimaera phantasma | Silver chimaera | Vulnerable (VU) | native |
| Pomacentridae | Chrysiptera hemicyanea | Azure demoiselle | Vulnerable (VU) | questionable |
| Clupeidae | Clupea manulensis | Critically Endangered (CR) | endemic | |
| 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 |
| Gobiidae | Elacatinus prochilos | Broadstripe goby | Vulnerable (VU) | questionable |
| 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 |
| Carcharhinidae | Glyphis gangeticus | Ganges shark | Critically Endangered (CR) | questionable |
| 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 |
| Pentanchidae | Halaelurus buergeri | Blackspotted catshark | Endangered (EN) | questionable |
| 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 | Hemitrygon bennettii | Bennett's stingray | Vulnerable (VU) | questionable |
| 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 |
| Lamnidae | Isurus paucus | Longfin mako | Endangered (EN) | questionable |
| Terapontidae | Leiopotherapon plumbeus | Vulnerable (VU) | endemic | |
| Lethrinidae | Lethrinus mahsena | Sky emperor | Endangered (EN) | questionable |
| Dasyatidae | Maculabatis gerrardi | Sharpnose stingray | Endangered (EN) | questionable |
| Dasyatidae | Maculabatis macrura | Endangered (EN) | native |