| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Davao Gulf | Sea/Bay/Gulf | native | 43437 |
| Indian Ocean | Sea/Bay/Gulf | native | 1602 |
| Indonesian Sea | Sea/Bay/Gulf | native | 1602 |
| Lanuza Bay | Sea/Bay/Gulf | native | 104756 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| North Australian Shelf | Sea/Bay/Gulf | native | 30874 |
| Pacific Ocean | Sea/Bay/Gulf | native | 1602 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 1602 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 53416 |
| Ulugan Bay | Sea/Bay/Gulf | native | 43468 |