| 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 | 48497 |
| Hsiao-liu-chiu | Sea/Bay/Gulf | native | 48451 |
| Indian Ocean | Sea/Bay/Gulf | native | 2334 |
| Indonesian Sea | Sea/Bay/Gulf | native | 5978 |
| Kuroshio Current | Sea/Bay/Gulf | native | 559 |
| Lanuza Bay | Sea/Bay/Gulf | native | 104756 |
| 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 |
| Peng-hu Island | Sea/Bay/Gulf | native | 55073 |
| Philippine Rise | Seamount | native | 116796 |
| Polynesian Waters | Sea/Bay/Gulf | native | 1602 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern China | Sea/Bay/Gulf | native | 128223 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 42484 |
| Tawi tawi Bay | Sea/Bay/Gulf | native | 59110 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 57038 |
| Yellow Sea | Sea/Bay/Gulf | native | 4868 |