| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Calamianes Islands | Sea/Bay/Gulf | native | 48613 |
| 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 | 48497 |
| Indian Ocean | Sea/Bay/Gulf | native | 55 |
| Indonesian Sea | Sea/Bay/Gulf | native | 55 |
| Kimbe Bay | Sea/Bay/Gulf | native | 28888 |
| Lagonoy Gulf | Sea/Bay/Gulf | native | 43283 |
| Milne Bay | Sea/Bay/Gulf | native | 41468 |
| North Australian Shelf | Sea/Bay/Gulf | native | 55 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 55 |
| Pacific Ocean | Sea/Bay/Gulf | native | 55 |
| Panay Gulf | Sea/Bay/Gulf | native | 42831 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern Palawan | Sea/Bay/Gulf | native | 58652 |
| Spratly Islands | Sea/Bay/Gulf | native | 48445 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 42484 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 57038 |
| Verde Island Passage | Sea/Bay/Gulf | native | 107854 |
| Yellow Sea | Sea/Bay/Gulf | native | 55 |