| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Calamianes Islands | Sea/Bay/Gulf | native | 48613 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 2334 |
| Dauin-Apo I. | Sea/Bay/Gulf | native | 127519 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 2334 |
| Indian Ocean | Sea/Bay/Gulf | native | 2334 |
| Indonesian Sea | Sea/Bay/Gulf | native | 2334 |
| Kimbe Bay | Sea/Bay/Gulf | native | 28888 |
| Lanuza Bay | Sea/Bay/Gulf | native | 104756 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| North Australian Shelf | Sea/Bay/Gulf | native | 2334 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 2334 |
| Northwest Australian Shelf | Sea/Bay/Gulf | native | 2334 |
| Pacific Ocean | Sea/Bay/Gulf | native | 2334 |
| Panguil Bay | Sea/Bay/Gulf | native | 47626 |
| Sogod Bay | Sea/Bay/Gulf | native | 46392 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern Palawan | Sea/Bay/Gulf | native | 2858 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 2858 |
| Tañon Strait | Sea/Bay/Gulf | native | 107276 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 53416 |
| Yellow Sea | Sea/Bay/Gulf | native | 12711 |