| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Andaman Sea | Sea/Bay/Gulf | native | 402 |
| Bay of Bengal | Sea/Bay/Gulf | native | 402 |
| Calamianes Islands | Sea/Bay/Gulf | native | 48613 |
| Dauin-Apo I. | Sea/Bay/Gulf | native | 127519 |
| Indian Ocean | Sea/Bay/Gulf | native | 402 |
| Indonesian Sea | Sea/Bay/Gulf | native | 402 |
| Kimbe Bay | Sea/Bay/Gulf | native | 28888 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| Pacific Ocean | Sea/Bay/Gulf | native | 402 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 402 |
| Tañon Strait | Sea/Bay/Gulf | native | |
| Tawi tawi Bay | Sea/Bay/Gulf | native | 59110 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 121724 |
| Verde Island Passage | Sea/Bay/Gulf | native | 107855 |