| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Calamianes Islands | Sea/Bay/Gulf | native | 48613 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 48497 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 48497 |
| Indian Ocean | Sea/Bay/Gulf | native | 7247 |
| Indonesian Sea | Sea/Bay/Gulf | native | 8631 |
| Kimbe Bay | Sea/Bay/Gulf | native | 28888 |
| Lingayen Gulf | Sea/Bay/Gulf | native | 5399 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| North Australian Shelf | Sea/Bay/Gulf | native | 2334 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 2334 |
| Northwest Australian Shelf | Sea/Bay/Gulf | native | 2334 |
| Pacific Ocean | Sea/Bay/Gulf | native | 2334 |
| Panay Gulf | Sea/Bay/Gulf | native | 42831 |
| Ragay Gulf | Sea/Bay/Gulf | native | 47919 |
| San Miguel Bay | Sea/Bay/Gulf | native | 45334 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern China | Sea/Bay/Gulf | native | 128223 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 6956 |
| Taal Lake | Lake | native | 12165 |
| Tayabas Bay | Sea/Bay/Gulf | native | 47588 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 53416 |
| Verde Island Passage | Sea/Bay/Gulf | native | 6956 |