| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agulhas Current | Sea/Bay/Gulf | native | 3145 |
| Calamianes Islands | Sea/Bay/Gulf | native | 48613 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 48497 |
| Dauin-Apo I. | Sea/Bay/Gulf | native | 127519 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 48497 |
| Indian Ocean | Sea/Bay/Gulf | native | 4974 |
| Indonesian Sea | Sea/Bay/Gulf | native | 4974 |
| Malalag Bay | Sea/Bay/Gulf | native | 106380 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| Pacific Ocean | Sea/Bay/Gulf | native | 5193 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Tañon Strait | Sea/Bay/Gulf | native | 10671 |
| Tawi tawi Bay | Sea/Bay/Gulf | native | 59110 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 53416 |
| Verde Island Passage | Sea/Bay/Gulf | native | 107629 |