| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agulhas Current | Sea/Bay/Gulf | native | 5213 |
| Andaman Sea | Sea/Bay/Gulf | native | 3433 |
| Arabian Sea | Sea/Bay/Gulf | native | 2872 |
| Atulayan Bay | Sea/Bay/Gulf | native | 41469 |
| Bay of Bengal | Sea/Bay/Gulf | native | 2108 |
| Carigara Bay | Sea/Bay/Gulf | native | 46323 |
| Chiku River | River (basin) | native | 36073 |
| Chilika Lake/Lagoon | Lagoon | native | 95460 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 3424 |
| Erhjen River | River (basin) | native | 36073 |
| Gulf of Aden | Sea/Bay/Gulf | native | 5450 |
| Gulf of Thailand | Sea/Bay/Gulf | native | 3432 |
| Honda Bay | Sea/Bay/Gulf | native | 71000 |
| Indian Ocean | Sea/Bay/Gulf | native | 3424 |
| Indonesian Sea | Sea/Bay/Gulf | native | 2108 |
| Kaoping River | River (basin) | native | 36073 |
| Lagonoy Gulf | Sea/Bay/Gulf | native | 43283 |
| Leyte Gulf | Sea/Bay/Gulf | native | 31411 |
| Lingayen Gulf | Sea/Bay/Gulf | native | 43020 |
| North Australian Shelf | Sea/Bay/Gulf | native | 3424 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 3424 |
| Northwest Australian Shelf | Sea/Bay/Gulf | native | 3424 |
| Ormoc Bay | Sea/Bay/Gulf | native | 45205 |
| Pacific Ocean | Sea/Bay/Gulf | native | 3424 |
| Pagbilao Bay | Sea/Bay/Gulf | native | 11338 |
| Panguil Bay | Sea/Bay/Gulf | native | 47626 |
| Peng-hu Island | Sea/Bay/Gulf | native | 55073 |
| Persian Gulf | Sea/Bay/Gulf | native | 3424 |
| Ragay Gulf | Sea/Bay/Gulf | native | 38601 |
| Red Sea | Sea/Bay/Gulf | native | 84159 |
| Ruerhmen River | River (basin) | native | 36073 |
| Samar Sea | Sea/Bay/Gulf | native | 29039 |
| San Miguel Bay | Sea/Bay/Gulf | native | 43275 |
| San Pedro Bay | Sea/Bay/Gulf | native | 46240 |
| Shihtsao River | River (basin) | native | 36073 |
| Shiliao River | River (basin) | native | 36073 |
| Sikao Creek | River (basin) | native | 52823 |
| Sogod Bay | Sea/Bay/Gulf | native | 46392 |
| Sorsogon Bay | Sea/Bay/Gulf | native | 47531 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern China | Sea/Bay/Gulf | native | 31075 |
| Southern Palawan | Sea/Bay/Gulf | native | 114805 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 2858 |
| Tayabas Bay | Sea/Bay/Gulf | native | 47573 |
| Tsengwen River | River (basin) | native | 36073 |
| Visayan Sea | Sea/Bay/Gulf | native | 3557 |
| Yellow Sea | Sea/Bay/Gulf | native | 5346 |