| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Calamianes Islands | Sea/Bay/Gulf | native | 48613 |
| Davao Gulf | Sea/Bay/Gulf | native | 45419 |
| Indonesian Sea | Sea/Bay/Gulf | native | 1602 |
| Kimbe Bay | Sea/Bay/Gulf | native | 28888 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| Moro Gulf | Sea/Bay/Gulf | native | 106380 |
| Pacific Ocean | Sea/Bay/Gulf | native | 1602 |
| San Miguel Bay | Sea/Bay/Gulf | native | 45334 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 45419 |
| Tañon Strait | Sea/Bay/Gulf | native | 107276 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 121724 |
| Verde Island Passage | Sea/Bay/Gulf | native | 107852 |