| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Andaman Sea | Sea/Bay/Gulf | native | 90102 |
| Calamianes Islands | Sea/Bay/Gulf | native | 48613 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 48497 |
| Davao Gulf | Sea/Bay/Gulf | native | 126188 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 48497 |
| Indian Ocean | Sea/Bay/Gulf | native | 2136 |
| Indonesian Sea | Sea/Bay/Gulf | native | 2136 |
| Kimbe Bay | Sea/Bay/Gulf | native | 28888 |
| Leyte Gulf | Sea/Bay/Gulf | native | 31411 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| North Australian Shelf | Sea/Bay/Gulf | native | 2334 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 2334 |
| Pacific Ocean | Sea/Bay/Gulf | native | 2334 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern Palawan | Sea/Bay/Gulf | native | 58652 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 2136 |
| Tawi tawi Bay | Sea/Bay/Gulf | native | 59110 |
| Tayabas Bay | Sea/Bay/Gulf | native | 47588 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 121724 |