| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Atulayan Bay | Sea/Bay/Gulf | native | 41469 |
| Calamianes Islands | Sea/Bay/Gulf | native | 48613 |
| Dauin-Apo I. | Sea/Bay/Gulf | native | 127519 |
| Indian Ocean | Sea/Bay/Gulf | native | 3412 |
| Indonesian Sea | Sea/Bay/Gulf | native | 5978 |
| Lagonoy Gulf | Sea/Bay/Gulf | native | 43283 |
| Lanuza Bay | Sea/Bay/Gulf | native | 104756 |
| Leyte Gulf | Sea/Bay/Gulf | native | 31411 |
| North Australian Shelf | Sea/Bay/Gulf | native | 3412 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 3412 |
| Northwest Australian Shelf | Sea/Bay/Gulf | native | 3412 |
| Pacific Ocean | Sea/Bay/Gulf | native | 3412 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 393 |