| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Calamianes Islands | Sea/Bay/Gulf | native | 48613 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 1602 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 2334 |
| Indian Ocean | Sea/Bay/Gulf | native | 2334 |
| Indonesian Sea | Sea/Bay/Gulf | native | 4859 |
| Kimbe Bay | Sea/Bay/Gulf | native | 28888 |
| Lingayen Gulf | Sea/Bay/Gulf | native | 46208 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| North Australian Shelf | Sea/Bay/Gulf | native | 1602 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 1602 |
| Northwest Australian Shelf | Sea/Bay/Gulf | native | 1602 |
| Pacific Ocean | Sea/Bay/Gulf | native | 1602 |
| Panay Gulf | Sea/Bay/Gulf | native | 42831 |
| Shark Bay | Sea/Bay/Gulf | native | 115274 |
| Shiliao River | River (basin) | native | 36073 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern Palawan | Sea/Bay/Gulf | native | 114805 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 393 |
| Tawi tawi Bay | Sea/Bay/Gulf | native | 59110 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 53416 |
| West Central Australian Shelf | Sea/Bay/Gulf | native | 115274 |
| Yellow Sea | Sea/Bay/Gulf | native | 5193 |