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It is well known that coral thermal bleaching is mainly caused by abnormally high temperatures, but the spatial/intergeneric variation in coral-algal symbiosis and its linkage to coral bleaching susceptibility is not well understood. In this study, 654 coral samples were collected from six coral reef regions (CRRs) in the South China Sea (SCS), between the Nansha Islands (similar to 10 degrees N) and Daya Bay (22 degrees 50N). They were analyzed to explore how geographical/environmental variation affects coral bleaching susceptibility. The results showed significant spatial and intergeneric variation in zooxanthellae density, Chl a content, and tissue biomass. Massive corals generally showed higher values than branching corals for all three parameters across CRRs. Spatial analysis showed that these parameters were lowest in the Nansha Islands and highest in Daya Bay, indicating increases with latitude. Several factors may have accounted for this trend, with the most important being sea surface temperature and nutrients. Additionally, we observed a relationship between physiological parameters and bleaching susceptibility, which was that branching corals had greater bleaching susceptibility than massive corals. Coral community composition and live coral cover data showing increasing dominance of massive corals in the SCS support the above inference. Relatively high-latitude areas have been proposed as potential refuges for corals under continued global warming and the physiological parameters in the present study seem to support this. However, in spite of the aforementioned results, the smallest live coral cover was found in the northern CRRs. This suggests that this refuge function is currently compromised, mainly due to increasing destructive anthropogenic actions.