Evolution of the marine protected area discourse into an area-based management tool may provide an avenue for a more progressive approach to protection of the Spratly seamounts. A first step could be the recognition of the Spratlys as an ecologically or biologically significant area (EBSA) under the Convention on Biological Diversity. This purely scientific recognition exercise would be without prejudice to the sovereignty, sovereign rights and jurisdiction of coastal States or State claiming sovereignty over the islands. Furthermore, it is up to the States concerned to later agree on specific restriction on activities in these areas as deemed necessary. This article shows that there are sufficient published data to justify that the Spratly seamounts meet the scientific criteria of an EBSA. However, it also proposes areas that may be prioritised on the basis of distinctive species composition of reef-building corals in the South China Sea.