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Climate change is the greatest threat to coral reef ecosystems. In particular, increasing ocean temperatures are causing severe and widespread coral bleaching, contributing to extensive coral loss and degradation of coral reef habitats globally. Effects of coral bleaching are not however, equally apportioned among different corals, leading to shifts in population and community structure. This study explored variation in bleaching susceptibility and mortality associated with the 2016 severe mass bleaching in the Central Maldives Archipelago. Five dominant coral taxa (tabular Acropora, Acropora humilis, Acropora muricata, Pocillopora and massive Porites) were surveyed in February 2016 and October 2017 to test for changes in abundance and size structure. Substantial taxonomic differences in rates of mortality were observed; the most severely affected taxa, Acropora, were virtually extirpated during the course of this study, whereas some other taxa (most notably, massive Porites) were relatively unaffected. However, even the least affected corals exhibited marked changes in population structure. In February 2016 (prior to recent mass-bleaching), size-frequency distributions of all coral taxa were dominated by larger size classes with over-centralized, peaked distributions (negatively skewed with positive kurtosis) reflecting a mature population structure. In October 2017, after the bleaching, coral populations were dominated by smaller and medium size classes, reflecting high levels of mortality and injury among larger coral colonies. Pronounced changes in coral populations and communities in the Maldives, caused by coral bleaching and other disturbances (outbreaks of crown-of-thorns starfish and sedimentation), will constrain recovery capacity, further compounding upon recent coral loss.