| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Bay of Bengal | Sea/Bay/Gulf | native | 5736 |
| Chiku River | River (basin) | native | 36073 |
| Chilika Lake/Lagoon | Lagoon | native | 95460 |
| Davao Gulf | Sea/Bay/Gulf | native | 43437 |
| East China Sea | Sea/Bay/Gulf | native | 47843 |
| Erhjen River | River (basin) | native | 36073 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 75154 |
| Gulf of Thailand | Sea/Bay/Gulf | native | 28029 |
| Indian Ocean | Sea/Bay/Gulf | native | 4323 |
| Indonesian Sea | Sea/Bay/Gulf | native | 5978 |
| Kaoping River | River (basin) | native | 36073 |
| Kimbe Bay | Sea/Bay/Gulf | native | 28888 |
| Lagonoy Gulf | Sea/Bay/Gulf | native | 43283 |
| Leyte Gulf | Sea/Bay/Gulf | native | 31411 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| North Australian Shelf | Sea/Bay/Gulf | native | 1602 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 1602 |
| Northwest Australian Shelf | Sea/Bay/Gulf | native | 1602 |
| Ormoc Bay | Sea/Bay/Gulf | native | 45140 |
| Pacific Ocean | Sea/Bay/Gulf | native | 1602 |
| Pagbilao Bay | Sea/Bay/Gulf | native | 11338 |
| Peng-hu Island | Sea/Bay/Gulf | native | 55073 |
| Ragay Gulf | Sea/Bay/Gulf | native | 47919 |
| 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 | 46241 |
| Shiliao River | River (basin) | native | 36073 |
| Sikao Creek | River (basin) | native | 52823 |
| Sogod Bay | Sea/Bay/Gulf | native | 31411 |
| 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 | 280 |
| Tayabas Bay | Sea/Bay/Gulf | native | 47573 |
| Tsengwen River | River (basin) | native | 36073 |
| Verde Island Passage | Sea/Bay/Gulf | native | 6956 |
| Yellow Sea | Sea/Bay/Gulf | native | 4868 |