| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Calamianes Islands | Sea/Bay/Gulf | native | 48613 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 2748 |
| Davao Gulf | Sea/Bay/Gulf | native | 45419 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 48497 |
| Indian Ocean | Sea/Bay/Gulf | native | 2334 |
| Indonesian Sea | Sea/Bay/Gulf | native | 2748 |
| Lanuza Bay | Sea/Bay/Gulf | native | 104756 |
| North Australian Shelf | Sea/Bay/Gulf | native | 2748 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 2748 |
| Pacific Ocean | Sea/Bay/Gulf | native | 2748 |
| Shark Bay | Sea/Bay/Gulf | native | 115274 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 2748 |
| Tawi tawi Bay | Sea/Bay/Gulf | native | 59110 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 53416 |
| Ulugan Bay | Sea/Bay/Gulf | native | 43468 |
| West Central Australian Shelf | Sea/Bay/Gulf | native | 115274 |