| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Andaman Sea | Sea/Bay/Gulf | native | 1419 |
| Arabian Sea | Sea/Bay/Gulf | native | 1419 |
| Bay of Bengal | Sea/Bay/Gulf | native | 1419 |
| Chilika Lake/Lagoon | Lagoon | native | 95460 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 1419 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 48497 |
| Gulf of Oman | Sea/Bay/Gulf | native | 11441 |
| Gulf of Thailand | Sea/Bay/Gulf | native | 1419 |
| Indian Ocean | Sea/Bay/Gulf | native | 1419 |
| Indonesian Sea | Sea/Bay/Gulf | native | 7050 |
| Lagonoy Gulf | Sea/Bay/Gulf | native | 43283 |
| Leyte Gulf | Sea/Bay/Gulf | native | 31411 |
| Lingayen Gulf | Sea/Bay/Gulf | native | 43020 |
| Lutao Island | Sea/Bay/Gulf | native | 11104 |
| Malacca Strait | Sea/Bay/Gulf | native | 121464 |
| North Australian Shelf | Sea/Bay/Gulf | native | 1419 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 1419 |
| Ormoc Bay | Sea/Bay/Gulf | native | 45140 |
| Pacific Ocean | Sea/Bay/Gulf | native | 1419 |
| Pagbilao Bay | Sea/Bay/Gulf | native | 11338 |
| Persian Gulf | Sea/Bay/Gulf | native | 1419 |
| Red Sea | Sea/Bay/Gulf | error | 84159 |
| Samar Sea | Sea/Bay/Gulf | native | 29039 |
| San Miguel Bay | Sea/Bay/Gulf | native | 43275 |
| Sikao Creek | River (basin) | native | 52823 |
| Sogod Bay | Sea/Bay/Gulf | native | 31411 |
| 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 | 130287 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 53416 |
| West Philippine Sea | Sea/Bay/Gulf | native | 130287 |