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The South China Sea in the Central Indo-Pacific is a large semi-enclosed marine region that supports an extraordinary diversity of coral reef organisms (including stony corals), which varies spatially across the region. While one-third of the world’s reef corals are known to face heightened extinction risk from global climate and local impacts, prospects for the coral fauna in the South China Sea region amidst these threats remain poorly understood. In this study, we analyse coral species richness, rarity, and phylogenetic diversity among 16 reef areas in the region to estimate changes in species and evolutionary diversity during projected anthropogenic extinctions. Our results show that richness, rarity, and phylogenetic diversity differ considerably among reef areas in the region, and that their outcomes following projected extinctions cannot be predicted by species diversity alone. Although relative rarity and threat levels are high in species-rich areas such as West Malaysia and the Philippines, areas with fewer species such as northern Vietnam and Paracel Islands stand to lose disproportionately large amounts of phylogenetic diversity. Our study quantifies various biodiversity components of each reef area to inform conservation planners and better direct sparse resources to areas where they are needed most. It also provides a critical biological foundation for targeting reefs that should be included in a regional network of marine protected areas in the South China Sea.

The South China Sea is an area of globally significant biological diversity. The Transboundary Diagnostic Analysis prepared for this marine basin identified the issue of coastal habitat degradation and loss as a key priority issue for action. The UNEP/GEF project entitled “ Reversing Environmental Degradation Trends in the South China Sea and Gulf of Thailand ” (SCS project) focused on these concerns through implementing a series of activities under the component on habitat degradation and loss. Important outputs of this project component were national reports on coastal habitats. This paper reviews and analyses available information from these reports and recent studies to present a review of the status and trends in coastal habitats of the South China Sea. This includes a technical summary of the best available information relating to the: distribution and extent of the dominant coastal habitats of mangroves, coral reefs, and seagrass; richness of habitat building species and hotspots of biodiversity; ranking of threats and the related rates of coastal habitat degradation and loss; and the state of coastal habitat management regimes. The use of this information in developing National Action Plans for habitats and the Strategic Action Programme for the South China Sea is reviewed. It is concluded that the science-based planning fostered by the SCS project was essential in reaching multi-lateral agreement on the regional targets and priority actions for coastal habitat management in this transboundary water body.