| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Coral Sea and GBR | Sea/Bay/Gulf | native | 48497 |
| Dauin-Apo I. | Sea/Bay/Gulf | native | 127519 |
| Davao Gulf | Sea/Bay/Gulf | native | 43437 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 42056 |
| 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 |
| Panay Gulf | Sea/Bay/Gulf | native | 42831 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 42484 |
| Tañon Strait | Sea/Bay/Gulf | native | 107276 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 53416 |
| Verde Island Passage | Sea/Bay/Gulf | native | 107629 |