| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Andaman Sea | Sea/Bay/Gulf | native | 2334 |
| Bay of Bengal | Sea/Bay/Gulf | native | 2334 |
| Calamianes Islands | Sea/Bay/Gulf | native | 48613 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 48497 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 40521 |
| Indian Ocean | Sea/Bay/Gulf | native | 2334 |
| Indonesian Sea | Sea/Bay/Gulf | native | 28620 |
| Lagonoy Gulf | Sea/Bay/Gulf | native | 43283 |
| 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 |
| Ragay Gulf | Sea/Bay/Gulf | native | 47919 |
| San Miguel Bay | Sea/Bay/Gulf | native | 45334 |
| San Pedro Bay | Sea/Bay/Gulf | native | 46241 |
| Sorsogon Bay | Sea/Bay/Gulf | native | 47531 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern Palawan | Sea/Bay/Gulf | native | 58652 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 393 |
| Tañon Strait | Sea/Bay/Gulf | native | 107276 |
| Tawi tawi Bay | Sea/Bay/Gulf | native | 59110 |
| Tayabas Bay | Sea/Bay/Gulf | native | 47588 |
| Yellow Sea | Sea/Bay/Gulf | native | 5193 |