| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Calamianes Islands | Sea/Bay/Gulf | native | 48613 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 402 |
| Davao Gulf | Sea/Bay/Gulf | native | 43437 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 402 |
| Gulf of Thailand | Sea/Bay/Gulf | native | 402 |
| Hsiao-liu-chiu | Sea/Bay/Gulf | native | 43515 |
| Indian Ocean | Sea/Bay/Gulf | native | 402 |
| Indonesian Sea | Sea/Bay/Gulf | native | 402 |
| Kimbe Bay | Sea/Bay/Gulf | native | 28888 |
| Lanuza Bay | Sea/Bay/Gulf | native | 104756 |
| Lutao Island | Sea/Bay/Gulf | native | 11104 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| North Australian Shelf | Sea/Bay/Gulf | native | 402 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 402 |
| Northwest Australian Shelf | Sea/Bay/Gulf | native | 402 |
| Pacific Ocean | Sea/Bay/Gulf | native | 402 |
| Peng-hu Island | Sea/Bay/Gulf | native | 43515 |
| San Pedro Bay | Sea/Bay/Gulf | native | 46241 |
| Shark Bay | Sea/Bay/Gulf | native | 115274 |
| Sogod Bay | Sea/Bay/Gulf | native | 31411 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern China | Sea/Bay/Gulf | native | 119494 |
| Southern Palawan | Sea/Bay/Gulf | native | 114805 |
| Spratly Islands | Sea/Bay/Gulf | native | 48445 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 402 |
| Tañon Strait | Sea/Bay/Gulf | native | 107276 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 121724 |
| Tung-hsiao | Sea/Bay/Gulf | native | 43515 |
| Ulugan Bay | Sea/Bay/Gulf | native | 43468 |
| West Central Australian Shelf | Sea/Bay/Gulf | native | 115274 |
| Yellow Sea | Sea/Bay/Gulf | native | 402 |