| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agulhas Current | Sea/Bay/Gulf | native | 55 |
| Andaman Sea | Sea/Bay/Gulf | native | 55 |
| Arabian Sea | Sea/Bay/Gulf | native | 55 |
| Atlantic Ocean | Sea/Bay/Gulf | native | 55 |
| Atulayan Bay | Sea/Bay/Gulf | native | 41469 |
| Australian | Zoogeographic realm | native | 55 |
| Bay of Bengal | Sea/Bay/Gulf | native | 55 |
| Calamianes Islands | Sea/Bay/Gulf | native | 48613 |
| Carigara Bay | Sea/Bay/Gulf | native | 46323 |
| Chiku River | River (basin) | native | 36073 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 55 |
| Dauin-Apo I. | Sea/Bay/Gulf | native | 127519 |
| Davao Gulf | Sea/Bay/Gulf | native | 106380 |
| East Central Australian Shelf | Sea/Bay/Gulf | native | 55 |
| Ethiopian | Zoogeographic realm | native | 114545 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 55 |
| Gulf of Aden | Sea/Bay/Gulf | native | 55 |
| Gulf of Thailand | Sea/Bay/Gulf | native | 55 |
| Hsiao-liu-chiu | Sea/Bay/Gulf | native | 48451 |
| Indian Ocean | Sea/Bay/Gulf | native | 55 |
| Indonesian Sea | Sea/Bay/Gulf | native | 55 |
| Insular Pacific-Hawaiian | Sea/Bay/Gulf | introduced | 55 |
| Kimbe Bay | Sea/Bay/Gulf | native | 28888 |
| Kuroshio Current | Sea/Bay/Gulf | native | 559 |
| Lagonoy Gulf | Sea/Bay/Gulf | native | 43283 |
| Lanuza Bay | Sea/Bay/Gulf | native | 104756 |
| Lingayen Gulf | Sea/Bay/Gulf | native | 5399 |
| Lutao Island | Sea/Bay/Gulf | native | 11104 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| Moro Gulf | Sea/Bay/Gulf | native | 106380 |
| North Australian Shelf | Sea/Bay/Gulf | native | 55 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 55 |
| Northwest Australian Shelf | Sea/Bay/Gulf | native | 55 |
| Oriental | Zoogeographic realm | native | 31075 |
| Ormoc Bay | Sea/Bay/Gulf | native | 45140 |
| Pacific Ocean | Sea/Bay/Gulf | native | 55 |
| Pagbilao Bay | Sea/Bay/Gulf | native | 11338 |
| Panay Gulf | Sea/Bay/Gulf | native | 42831 |
| Peng-hu Island | Sea/Bay/Gulf | native | 55073 |
| Persian Gulf | Sea/Bay/Gulf | questionable | 114545 |
| Polynesian Waters | Sea/Bay/Gulf | native | 55 |
| Ragay Gulf | Sea/Bay/Gulf | native | 47919 |
| Red Sea | Sea/Bay/Gulf | questionable | 114545 |
| Ruerhmen River | River (basin) | native | 36073 |
| San Miguel Bay | Sea/Bay/Gulf | native | 45161 |
| Shiliao River | River (basin) | native | 36073 |
| Socotra Archipelago | Sea/Bay/Gulf | native | 37631 |
| Sogod Bay | Sea/Bay/Gulf | native | 46392 |
| Somali Coastal Current | Sea/Bay/Gulf | native | 55 |
| Sorsogon Bay | Sea/Bay/Gulf | native | 47531 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern China | Sea/Bay/Gulf | native | 119494 |
| Southern Palawan | Sea/Bay/Gulf | native | 114805 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 42419 |
| Tahiti I. | Sea/Bay/Gulf | native | 55 |
| Tañon Strait | Sea/Bay/Gulf | native | 107276 |
| Tayabas Bay | Sea/Bay/Gulf | native | 47573 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 53416 |
| Verde Island Passage | Sea/Bay/Gulf | native | 107853 |
| Yellow Sea | Sea/Bay/Gulf | native | 55 |