| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agulhas Current | Sea/Bay/Gulf | native | 5213 |
| Atulayan Bay | Sea/Bay/Gulf | native | 41469 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 4859 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 2334 |
| Hsiao-liu-chiu | Sea/Bay/Gulf | native | 48445 |
| Indian Ocean | Sea/Bay/Gulf | native | 2334 |
| Indonesian Sea | Sea/Bay/Gulf | native | 5978 |
| Kimbe Bay | Sea/Bay/Gulf | native | 28888 |
| Kuroshio Current | Sea/Bay/Gulf | native | 559 |
| Lanuza Bay | Sea/Bay/Gulf | native | 104756 |
| Lutao Island | Sea/Bay/Gulf | native | 11104 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| North Australian Shelf | Sea/Bay/Gulf | native | 4859 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 4859 |
| Northwest Australian Shelf | Sea/Bay/Gulf | native | 4859 |
| Pacific Ocean | Sea/Bay/Gulf | native | 33390 |
| Panay Gulf | Sea/Bay/Gulf | native | 42831 |
| Peng-hu Island | Sea/Bay/Gulf | native | 55073 |
| Sarangani Bay | Sea/Bay/Gulf | native | 106380 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Spratly Islands | Sea/Bay/Gulf | native | 48445 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 42484 |
| Tawi tawi Bay | Sea/Bay/Gulf | native | 59110 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 57038 |
| Verde Island Passage | Sea/Bay/Gulf | native | 6956 |
| Yellow Sea | Sea/Bay/Gulf | native | 5193 |