| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Andaman Sea | Sea/Bay/Gulf | native | 37792 |
| Calamianes Islands | Sea/Bay/Gulf | native | 48613 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 48497 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 37816 |
| Indian Ocean | Sea/Bay/Gulf | native | 9710 |
| Indonesian Sea | Sea/Bay/Gulf | native | 1602 |
| Kimbe Bay | Sea/Bay/Gulf | native | 28888 |
| Lanuza Bay | Sea/Bay/Gulf | native | 104756 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| Pacific Ocean | Sea/Bay/Gulf | native | 4868 |
| Philippine Rise | Seamount | native | 116796 |
| San Miguel Bay | Sea/Bay/Gulf | native | 45334 |
| Sarangani Bay | Sea/Bay/Gulf | native | 106380 |
| Sogod Bay | Sea/Bay/Gulf | native | 46392 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern Palawan | Sea/Bay/Gulf | native | 58652 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 42419 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 53416 |
| Yellow Sea | Sea/Bay/Gulf | native | 4868 |