| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Andaman Sea | Sea/Bay/Gulf | native | 402 |
| Bay of Bengal | Sea/Bay/Gulf | native | 402 |
| Calamianes Islands | Sea/Bay/Gulf | native | 48613 |
| Dauin-Apo I. | Sea/Bay/Gulf | native | 127519 |
| Davao Gulf | Sea/Bay/Gulf | native | 106380 |
| Gulf of Thailand | Sea/Bay/Gulf | native | 402 |
| Indian Ocean | Sea/Bay/Gulf | native | 402 |
| Indonesian Sea | Sea/Bay/Gulf | native | 402 |
| Kimbe Bay | Sea/Bay/Gulf | native | 28888 |
| Kuroshio Current | Sea/Bay/Gulf | native | 559 |
| Lagonoy Gulf | Sea/Bay/Gulf | native | 43283 |
| Lingayen Gulf | Sea/Bay/Gulf | native | 5399 |
| Malalag Bay | Sea/Bay/Gulf | native | 106380 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| Moro Gulf | Sea/Bay/Gulf | native | 106380 |
| Ormoc Bay | Sea/Bay/Gulf | native | 45205 |
| Pacific Ocean | Sea/Bay/Gulf | native | 402 |
| Panay Gulf | Sea/Bay/Gulf | native | 42831 |
| Ragay Gulf | Sea/Bay/Gulf | native | 47919 |
| Red Sea | Sea/Bay/Gulf | error | 84159 |
| San Miguel Bay | Sea/Bay/Gulf | native | 45334 |
| Sogod Bay | Sea/Bay/Gulf | native | 46392 |
| Somali Coastal Current | Sea/Bay/Gulf | native | 402 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern Palawan | Sea/Bay/Gulf | native | 114805 |
| Spratly Islands | Sea/Bay/Gulf | native | 48445 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 42484 |
| Tañon Strait | Sea/Bay/Gulf | native | |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 121724 |
| Verde Island Passage | Sea/Bay/Gulf | native | 42643 |
| Yellow Sea | Sea/Bay/Gulf | native | 559 |