| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Coral Sea and GBR | Sea/Bay/Gulf | native | 1602 |
| Dauin-Apo I. | Sea/Bay/Gulf | native | 127519 |
| Davao Gulf | Sea/Bay/Gulf | native | 43437 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 9823 |
| Hsiao-liu-chiu | Sea/Bay/Gulf | native | 48445 |
| Kimbe Bay | Sea/Bay/Gulf | native | 28888 |
| Lutao Island | Sea/Bay/Gulf | native | 11104 |
| Malalag Bay | Sea/Bay/Gulf | native | 106380 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| Moro Gulf | Sea/Bay/Gulf | native | 106380 |
| Pacific Ocean | Sea/Bay/Gulf | native | 128223 |
| Panay Gulf | Sea/Bay/Gulf | native | 42831 |
| Peng-hu Island | Sea/Bay/Gulf | native | 55073 |
| 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 China | Sea/Bay/Gulf | native | 128223 |
| Spratly Islands | Sea/Bay/Gulf | native | 48445 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 45419 |
| Tañon Strait | Sea/Bay/Gulf | native | 107276 |
| Tawi tawi Bay | Sea/Bay/Gulf | native | 59110 |
| Tayabas Bay | Sea/Bay/Gulf | native | 47588 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 53416 |
| Verde Island Passage | Sea/Bay/Gulf | native | 107629 |