| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Agulhas Current | Sea/Bay/Gulf | native | 3488 |
| Dauin-Apo I. | Sea/Bay/Gulf | native | 127519 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 75154 |
| Indian Ocean | Sea/Bay/Gulf | native | 3488 |
| Indonesian Sea | Sea/Bay/Gulf | native | 8631 |
| Kimbe Bay | Sea/Bay/Gulf | native | 28888 |
| Kuroshio Current | Sea/Bay/Gulf | native | 559 |
| Lingayen Gulf | Sea/Bay/Gulf | native | 5399 |
| Malalag Bay | Sea/Bay/Gulf | native | 106380 |
| Milne Bay | Sea/Bay/Gulf | native | 41464 |
| Pacific Ocean | Sea/Bay/Gulf | native | 592 |
| Polynesian Waters | Sea/Bay/Gulf | native | 3488 |
| Sarangani Bay | Sea/Bay/Gulf | native | 106380 |
| Sogod Bay | Sea/Bay/Gulf | native | 46392 |
| Somali Coastal Current | Sea/Bay/Gulf | native | 3488 |
| South China Sea | Sea/Bay/Gulf | native | 36648 |
| Southern Palawan | Sea/Bay/Gulf | native | 58652 |
| Sulu-Celebes Sea | Sea/Bay/Gulf | native | 130287 |
| Tañon Strait | Sea/Bay/Gulf | native | 107276 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 121724 |
| West Philippine Sea | Sea/Bay/Gulf | native | 130287 |
| West Philippine Sea | Sea/Bay/Gulf | native | 5399 |