| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Atulayan Bay | Sea/Bay/Gulf | native | 41469 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 48497 |
| East Central Australian Shelf | Sea/Bay/Gulf | native | 3132 |
| East China Sea | Sea/Bay/Gulf | native | 47843 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 48497 |
| Indian Ocean | Sea/Bay/Gulf | native | 9710 |
| Indonesian Sea | Sea/Bay/Gulf | native | 559 |
| Kuroshio Current | Sea/Bay/Gulf | native | 559 |
| North Australian Shelf | Sea/Bay/Gulf | native | 3132 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 3132 |
| Northwest Australian Shelf | Sea/Bay/Gulf | native | 3132 |
| Pacific Ocean | Sea/Bay/Gulf | native | 3132 |
| Pagbilao Bay | Sea/Bay/Gulf | native | 11338 |
| Peng-hu Island | Sea/Bay/Gulf | native | 55073 |
| Shiliao River | River (basin) | native | 36073 |
| Sikao Creek | River (basin) | native | 52823 |
| Sorsogon Bay | Sea/Bay/Gulf | native | 47531 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern Palawan | Sea/Bay/Gulf | native | 58652 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 5454 |
| Tawi tawi Bay | Sea/Bay/Gulf | native | 59110 |
| Yellow Sea | Sea/Bay/Gulf | native | 5193 |