| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agulhas Current | Sea/Bay/Gulf | native | 5213 |
| Arabian Sea | Sea/Bay/Gulf | native | 2872 |
| Arafura Sea | Sea/Bay/Gulf | native | 9819 |
| Bay of Bengal | Sea/Bay/Gulf | native | 5736 |
| Chiku River | River (basin) | native | 36073 |
| Davao Gulf | Sea/Bay/Gulf | native | 43437 |
| East China Sea | Sea/Bay/Gulf | native | 47843 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 75154 |
| Gulf of Oman | Sea/Bay/Gulf | native | 47533 |
| Gulf of Thailand | Sea/Bay/Gulf | native | 1632 |
| Indian Ocean | Sea/Bay/Gulf | native | 4375 |
| Indonesian Sea | Sea/Bay/Gulf | native | 5978 |
| Lagonoy Gulf | Sea/Bay/Gulf | native | 43283 |
| Lanuza Bay | Sea/Bay/Gulf | native | 104756 |
| Lingayen Gulf | Sea/Bay/Gulf | native | 43020 |
| Manila Bay | Sea/Bay/Gulf | native | 35686 |
| North Australian Shelf | Sea/Bay/Gulf | native | 5978 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 5978 |
| Northwest Australian Shelf | Sea/Bay/Gulf | native | 5978 |
| Ormoc Bay | Sea/Bay/Gulf | native | 45205 |
| Pacific Ocean | Sea/Bay/Gulf | native | 5978 |
| Panguil Bay | Sea/Bay/Gulf | native | 47626 |
| Peng-hu Island | Sea/Bay/Gulf | native | 55073 |
| Persian Gulf | Sea/Bay/Gulf | native | 11441 |
| Red Sea | Sea/Bay/Gulf | error | 84159 |
| Samar Sea | Sea/Bay/Gulf | native | 29039 |
| San Miguel Bay | Sea/Bay/Gulf | native | 43275 |
| San Pedro Bay | Sea/Bay/Gulf | native | 46241 |
| Sogod Bay | Sea/Bay/Gulf | native | 46392 |
| Somali Coastal Current | Sea/Bay/Gulf | native | 12484 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern China | Sea/Bay/Gulf | native | 119494 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 280 |
| Tayabas Bay | Sea/Bay/Gulf | native | 82367 |
| Verde Island Passage | Sea/Bay/Gulf | native | 82367 |
| Yellow Sea | Sea/Bay/Gulf | questionable | 47690 |