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Sea surface temperatures were warmer throughout 1998 at Sesoko Island, Japan, than in the 10 preceding years. Temperatures peaked at 2.8 °C above average, resulting in extensive coral bleaching and subsequent coral mortality. Using random quadrat surveys, we quantitatively documented the coral community structure one year before and one year after the bleaching event. The 1998 bleaching event reduced coral species richness by 61% and reduced coral cover by 85%. Colony morphology affected bleaching vulnerability and subsequent coral mortality. Finely branched corals were most susceptible, while massive and encrusting colonies survived. Most heavily impacted were the branched Acropora and pocilloporid corals, some of which showed local extinction. We suggest two hypotheses whose synergistic effect may partially explain observed mortality patterns (i.e. preferential survival of thick‐tissued species, and shape‐dependent differences in colony mass‐transfer efficiency). A community‐structural shift occurred on Okinawan reefs, resulting in an increase in the relative abundance of massive and encrusting coral species.