| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Andaman Sea | Sea/Bay/Gulf | native | 846 |
| Arafura Sea | Sea/Bay/Gulf | native | 846 |
| Banda Sea | Sea/Bay/Gulf | native | 846 |
| Bay of Bengal | Sea/Bay/Gulf | native | 846 |
| Bismarck Sea | Sea/Bay/Gulf | native | 846 |
| Central Indo-Pacific | sea/bay/gulf | native | 846 |
| Eastern Coral Triangle | sea/bay/gulf | native | 89710 |
| Eastern Philippines | Sea/Bay/Gulf | native | 846 |
| Halmahera | Sea/Bay/Gulf | native | 846 |
| Indian Ocean | Sea/Bay/Gulf | native | 846 |
| Indonesian Sea | Sea/Bay/Gulf | native | 846 |
| Lesser Sunda | Sea/Bay/Gulf | native | 846 |
| Malacca Strait | Sea/Bay/Gulf | native | 846 |
| Northeast Sulawesi | Sea/Bay/Gulf | native | 846 |
| Pacific Ocean | Sea/Bay/Gulf | native | 846 |
| Palawan/North Borneo | Sea/Bay/Gulf | native | 846 |
| Papua | Sea/Bay/Gulf | native | 846 |
| Solomon Archipelago | Sea/Bay/Gulf | native | 89710 |
| Solomon Sea | Sea/Bay/Gulf | native | 75728 |
| South China Sea | Sea/Bay/Gulf | native | 846 |
| Southern Java | Sea/Bay/Gulf | native | 846 |
| Sulawesi Sea/Makassar Strait | Sea/Bay/Gulf | native | 846 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 846 |
| Sunda Shelf/Java Sea | Sea/Bay/Gulf | native | 846 |
| Tropical Northwestern Pacific | sea/bay/gulf | native | 103508 |
| West Caroline Islands | Sea/Bay/Gulf | native | 103508 |
| West Philippine Sea | Sea/Bay/Gulf | native | 846 |
| Western Coral Triangle | sea/bay/gulf | native | 846 |
| Western Sumatra | Sea/Bay/Gulf | native | 846 |