| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Calamianes Islands | Sea/Bay/Gulf | native | 48613 |
| Dauin-Apo I. | Sea/Bay/Gulf | native | 127519 |
| Indian Ocean | Sea/Bay/Gulf | native | 1602 |
| Indonesian Sea | Sea/Bay/Gulf | native | 8631 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| Moro Gulf | Sea/Bay/Gulf | native | 106380 |
| North Australian Shelf | Sea/Bay/Gulf | native | 1602 |
| Northwest Australian Shelf | Sea/Bay/Gulf | native | 1602 |
| Pacific Ocean | Sea/Bay/Gulf | native | 1602 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 130287 |
| Tawi tawi Bay | Sea/Bay/Gulf | native | 59110 |
| West Philippine Sea | Sea/Bay/Gulf | native | 130287 |