| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agulhas Current | Sea/Bay/Gulf | native | 5213 |
| Bataraza | Sea/Bay/Gulf | native | 114805 |
| Brooke's Point | Sea/Bay/Gulf | native | 114805 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 7300 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 3197 |
| Indian Ocean | Sea/Bay/Gulf | native | 3197 |
| Indonesian Sea | Sea/Bay/Gulf | native | 3280 |
| Kimbe Bay | Sea/Bay/Gulf | native | 28888 |
| Kuroshio Current | Sea/Bay/Gulf | native | 559 |
| Lagonoy Gulf | Sea/Bay/Gulf | native | 43283 |
| North Australian Shelf | Sea/Bay/Gulf | native | 7300 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 7300 |
| Northwest Australian Shelf | Sea/Bay/Gulf | native | 7300 |
| Pacific Ocean | Sea/Bay/Gulf | native | 3280 |
| Ragay Gulf | Sea/Bay/Gulf | native | 47919 |
| San Miguel Bay | Sea/Bay/Gulf | native | 43275 |
| Sofronio Española | Sea/Bay/Gulf | native | 114805 |
| Sogod Bay | Sea/Bay/Gulf | native | 46392 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern Palawan | Sea/Bay/Gulf | native | 58652 |
| Tanshui River | River (basin) | native | 36073 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 53416 |
| Yellow Sea | Sea/Bay/Gulf | native | 5193 |