| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Andaman Sea | Sea/Bay/Gulf | native | 2295 |
| Bay of Bengal | Sea/Bay/Gulf | native | 2295 |
| Calamianes Islands | Sea/Bay/Gulf | native | 48613 |
| Carigara Bay | Sea/Bay/Gulf | native | 46323 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 48497 |
| Dauin-Apo I. | Sea/Bay/Gulf | native | 127519 |
| Davao Gulf | Sea/Bay/Gulf | native | 126188 |
| East China Sea | Sea/Bay/Gulf | native | 37816 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 48497 |
| Indian Ocean | Sea/Bay/Gulf | native | 2295 |
| Indonesian Sea | Sea/Bay/Gulf | native | 2295 |
| Kimbe Bay | Sea/Bay/Gulf | native | 28888 |
| Lagonoy Gulf | Sea/Bay/Gulf | native | 43283 |
| Leyte Gulf | Sea/Bay/Gulf | native | 31411 |
| Lingayen Gulf | Sea/Bay/Gulf | native | 5399 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| North Australian Shelf | Sea/Bay/Gulf | native | 2295 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 2295 |
| Ormoc Bay | Sea/Bay/Gulf | native | 45205 |
| Pacific Ocean | Sea/Bay/Gulf | native | 2295 |
| Peng-hu Island | Sea/Bay/Gulf | native | 55073 |
| San Miguel Bay | Sea/Bay/Gulf | native | 43275 |
| Sogod Bay | Sea/Bay/Gulf | native | 46392 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern China | Sea/Bay/Gulf | native | 94637 |
| Southern Palawan | Sea/Bay/Gulf | native | 114805 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 2295 |
| Tañon Strait | Sea/Bay/Gulf | native | 107276 |
| Tayabas Bay | Sea/Bay/Gulf | native | 82367 |
| Verde Island Passage | Sea/Bay/Gulf | native | 6956 |