| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agulhas Current | Sea/Bay/Gulf | native | 5213 |
| Andaman Sea | Sea/Bay/Gulf | native | 45255 |
| Arabian Sea | Sea/Bay/Gulf | native | 3287 |
| Atlantic Ocean | Sea/Bay/Gulf | native | 3287 |
| Atulayan Bay | Sea/Bay/Gulf | native | 41469 |
| Bay of Bengal | Sea/Bay/Gulf | native | 3287 |
| Brooke's Point | Sea/Bay/Gulf | native | 114805 |
| Carigara Bay | Sea/Bay/Gulf | native | 46323 |
| Dauin-Apo I. | Sea/Bay/Gulf | native | 127519 |
| Erhjen River | River (basin) | native | 36073 |
| Gulf of Aden | Sea/Bay/Gulf | native | 3287 |
| Gulf of Oman | Sea/Bay/Gulf | native | 3287 |
| Gulf of Thailand | Sea/Bay/Gulf | native | 11441 |
| Honda Bay | Sea/Bay/Gulf | native | 71000 |
| Indian Ocean | Sea/Bay/Gulf | native | 3287 |
| Indonesian Sea | Sea/Bay/Gulf | native | 4899 |
| Ormoc Bay | Sea/Bay/Gulf | native | 45205 |
| Pacific Ocean | Sea/Bay/Gulf | native | 3287 |
| Peng-hu Island | Sea/Bay/Gulf | native | 55073 |
| Persian Gulf | Sea/Bay/Gulf | native | 3287 |
| Ragay Gulf | Sea/Bay/Gulf | native | 38601 |
| Red Sea | Sea/Bay/Gulf | native | 84159 |
| Sogod Bay | Sea/Bay/Gulf | native | 31411 |
| Somali Coastal Current | Sea/Bay/Gulf | native | 3287 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern China | Sea/Bay/Gulf | native | 94637 |
| Southern Palawan | Sea/Bay/Gulf | native | 114805 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 3287 |
| Tung-hsiao | Sea/Bay/Gulf | native | 43510 |
| Visayan Sea | Sea/Bay/Gulf | native | 110390 |
| Yellow Sea | Sea/Bay/Gulf | native | 3287 |