| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agulhas Current | Sea/Bay/Gulf | native | 5213 |
| Andaman Sea | Sea/Bay/Gulf | native | 2116 |
| Arabian Sea | Sea/Bay/Gulf | native | 2872 |
| Atlantic Ocean | Sea/Bay/Gulf | native | 5491 |
| Bay of Bengal | Sea/Bay/Gulf | native | 2116 |
| Carigara Bay | Sea/Bay/Gulf | native | 46323 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 2116 |
| Davao Gulf | Sea/Bay/Gulf | native | 43437 |
| East China Sea | Sea/Bay/Gulf | native | 37816 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 5491 |
| Gulf of Aden | Sea/Bay/Gulf | native | 4752 |
| Gulf of Oman | Sea/Bay/Gulf | native | 4752 |
| Gulf of Thailand | Sea/Bay/Gulf | native | 2116 |
| Indian Ocean | Sea/Bay/Gulf | native | 5491 |
| Indonesian Sea | Sea/Bay/Gulf | native | 7050 |
| Kimbe Bay | Sea/Bay/Gulf | native | 28888 |
| Lagonoy Gulf | Sea/Bay/Gulf | native | 43283 |
| Leyte Gulf | Sea/Bay/Gulf | native | 68980 |
| Lingayen Gulf | Sea/Bay/Gulf | native | 5399 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| North Australian Shelf | Sea/Bay/Gulf | native | 2116 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 2116 |
| Northwest Australian Shelf | Sea/Bay/Gulf | native | 2116 |
| Ormoc Bay | Sea/Bay/Gulf | native | 45140 |
| Pacific Ocean | Sea/Bay/Gulf | native | 2116 |
| Peng-hu Island | Sea/Bay/Gulf | native | 55073 |
| Persian Gulf | Sea/Bay/Gulf | native | 4752 |
| Ragay Gulf | Sea/Bay/Gulf | native | 47919 |
| Red Sea | Sea/Bay/Gulf | native | 84159 |
| Samar Sea | Sea/Bay/Gulf | native | 29039 |
| San Miguel Bay | Sea/Bay/Gulf | native | 43275 |
| San Pedro Bay | Sea/Bay/Gulf | native | 46240 |
| Somali Coastal Current | Sea/Bay/Gulf | native | 4752 |
| Sorsogon Bay | Sea/Bay/Gulf | native | 47531 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern Palawan | Sea/Bay/Gulf | native | 114805 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 2858 |
| Tayabas Bay | Sea/Bay/Gulf | native | 47573 |
| Verde Island Passage | Sea/Bay/Gulf | native | 107853 |
| Chiku River | River (basin) | native | 36073 |
| Ruerhmen River | River (basin) | native | 36073 |
| Shihtsao River | River (basin) | native | 36073 |
| Shiliao River | River (basin) | native | 36073 |
| Sikao Creek | River (basin) | native | 52823 |
| Tsengwen River | River (basin) | native | 36073 |
| Chilika Lake/Lagoon | Lagoon | native | 95460 |