| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Calamianes Islands | Sea/Bay/Gulf | native | 48613 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 48497 |
| Davao Gulf | Sea/Bay/Gulf | native | 43437 |
| 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 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| Moro Gulf | Sea/Bay/Gulf | native | 106380 |
| North Australian Shelf | Sea/Bay/Gulf | native | 7247 |
| Northwest Australian Shelf | Sea/Bay/Gulf | native | 7247 |
| Pacific Ocean | Sea/Bay/Gulf | native | 7247 |
| Ragay Gulf | Sea/Bay/Gulf | native | 47919 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 42484 |
| Tañon Strait | Sea/Bay/Gulf | native | 107276 |
| Tawi tawi Bay | Sea/Bay/Gulf | native | 59110 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 57038 |
| Verde Island Passage | Sea/Bay/Gulf | native | 107852 |