| Family | Species | FishBase name | Threat Category | Occurrence |
|---|---|---|---|---|
| Triakidae | Hemitriakis leucoperiptera | Whitefin topeshark | Endangered (EN) | endemic |
| Dasyatidae | Himantura leoparda | Vulnerable (VU) | native | |
| Dasyatidae | Himantura uarnak | Honeycomb stingray | Vulnerable (VU) | 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 | Vulnerable (VU) | native |
| Myliobatidae | Manta alfredi | Alfred manta | Vulnerable (VU) | native |
| Myliobatidae | Manta birostris | Giant manta | Vulnerable (VU) | native |
| Syngnathidae | Microphis pleurostictus | Endangered (EN) | endemic | |
| Myliobatidae | Mobula tarapacana | Chilean devil ray | Vulnerable (VU) | native |
| Molidae | Mola mola | Ocean sunfish | Vulnerable (VU) | native |
| Ginglymostomatidae | Nebrius ferrugineus | Tawny nurse shark | Vulnerable (VU) | native |
| Carcharhinidae | Negaprion acutidens | Sicklefin lemon shark | Vulnerable (VU) | native |
| Nemipteridae | Nemipterus virgatus | Golden threadfin bream | Vulnerable (VU) | native |
| Phallostethidae | Neostethus thessa | Endangered (EN) | endemic | |
| Monacanthidae | Oxymonacanthus longirostris | Harlequin filefish | Vulnerable (VU) | native |
| Gobiidae | Pandaka pygmaea | Dwarf pygmy goby | Critically Endangered (CR) | native |
| Bythitidae | Paradiancistrus cuyoensis | Cuyo coralbrotula | Vulnerable (VU) | endemic |
| Serranidae | Plectropomus areolatus | Squaretail coralgrouper | Vulnerable (VU) | native |
| Serranidae | Plectropomus laevis | Blacksaddled coralgrouper | Vulnerable (VU) | native |
| Pristidae | Pristis zijsron | Longcomb sawfish | Critically Endangered (CR) | native |
| Rhinidae | Rhina ancylostoma | Bowmouth guitarfish | Vulnerable (VU) | native |
| Rhincodontidae | Rhincodon typus | Whale shark | Endangered (EN) | native |
| Myliobatidae | Rhinoptera javanica | Flapnose ray | Vulnerable (VU) | native |
| Rhinidae | Rhynchobatus australiae | Bottlenose wedgefish | Vulnerable (VU) | native |
| Rhinidae | Rhynchobatus springeri | Broadnose wedgefish | Vulnerable (VU) | native |
| Gobiidae | Sicyopus auxilimentus | Vulnerable (VU) | endemic | |
| Sphyrnidae | Sphyrna lewini | Scalloped hammerhead | Endangered (EN) | native |
| Sphyrnidae | Sphyrna mokarran | Great hammerhead | Endangered (EN) | native |
| Sphyrnidae | Sphyrna zygaena | Smooth hammerhead | Vulnerable (VU) | native |
| Squalidae | Squalus montalbani | Indonesian greeneye spurdog | Vulnerable (VU) | native |
| Stegostomatidae | Stegostoma fasciatum | Zebra shark | Endangered (EN) | native |
| Gobiidae | Stiphodon surrufus | Vulnerable (VU) | endemic | |
| Engraulidae | Stolephorus ronquilloi | Ronquillo's anchovy | Vulnerable (VU) | endemic |
| Dasyatidae | Taeniurops meyeni | Round ribbontail ray | Vulnerable (VU) | native |
| Scombridae | Thunnus obesus | Bigeye tuna | Vulnerable (VU) | native |
| Scombridae | Thunnus orientalis | Pacific bluefin tuna | Vulnerable (VU) | native |
| Dasyatidae | Urogymnus asperrimus | Porcupine whipray | Vulnerable (VU) | native |
| Soleidae | Zebrias lucapensis | Vulnerable (VU) | endemic |