| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Aborlan | Sea/Bay/Gulf | native | 114805 |
| Agulhas Current | Sea/Bay/Gulf | native | 1920 |
| Andaman Sea | Sea/Bay/Gulf | native | 37792 |
| Arabian Sea | Sea/Bay/Gulf | native | 45255 |
| Calamianes Islands | Sea/Bay/Gulf | native | 48613 |
| Chilika Lake/Lagoon | Lagoon | native | 95460 |
| Coral Sea and GBR | Sea/Bay/Gulf | native | 2334 |
| Dauin-Apo I. | Sea/Bay/Gulf | native | 127519 |
| Davao Gulf | Sea/Bay/Gulf | native | 45419 |
| Great Barrier Reef | Sea/Bay/Gulf | native | 37792 |
| Hsiao-liu-chiu | Sea/Bay/Gulf | native | 48445 |
| Indian Ocean | Sea/Bay/Gulf | native | 1602 |
| Indonesian Sea | Sea/Bay/Gulf | native | 5978 |
| 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 |
| Moro Gulf | Sea/Bay/Gulf | native | 106380 |
| Narra | Sea/Bay/Gulf | native | 114805 |
| North Australian Shelf | Sea/Bay/Gulf | native | 2334 |
| Northeast Australian Shelf | Sea/Bay/Gulf | native | 2334 |
| Northwest Australian Shelf | Sea/Bay/Gulf | native | 37792 |
| Pacific Ocean | Sea/Bay/Gulf | native | 592 |
| Peng-hu Island | Sea/Bay/Gulf | native | 48445 |
| Polynesian Waters | Sea/Bay/Gulf | native | 4795 |
| Ragay Gulf | Sea/Bay/Gulf | native | 47919 |
| Red Sea | Sea/Bay/Gulf | native | 84159 |
| Ruerhmen River | River (basin) | native | 36073 |
| San Miguel Bay | Sea/Bay/Gulf | native | 45334 |
| Sarangani Bay | Sea/Bay/Gulf | native | 106380 |
| Shiliao River | River (basin) | native | 36073 |
| Sofronio Española | Sea/Bay/Gulf | native | 114805 |
| Sogod Bay | Sea/Bay/Gulf | native | 46392 |
| 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 |
| Tahiti I. | Sea/Bay/Gulf | native | 4795 |
| Tayabas Bay | Sea/Bay/Gulf | native | 47588 |
| Tubbataha Reefs | Sea/Bay/Gulf | native | 57038 |
| Verde Island Passage | Sea/Bay/Gulf | native | 37603 |
| Yellow Sea | Sea/Bay/Gulf | native | 5193 |