Complex histories of chronic and acute sea surface temperature (SST) stresses are expected to trigger taxon- and location-specific responses that will ultimately lead to novel coral communities. The 2016 El Niño-Southern Oscillation provided an opportunity to examine large-scale and recent environmental histories on emerging patterns in 226 coral communities distributed across 12 countries from East Africa to Fiji. Six main coral communities were identified that largely varied across a gradient of Acropora to massive Porites dominance. Bleaching intensity was taxon-specific and was associated with complex interactions among the 20 environmental variables that we examined. Coral community structure was better aligned with the historical temperature patterns between 1985 and 2015 than the 2016 extreme temperature event. Additionally, bleaching responses observed during 2016 differed from historical reports during past warm years. Consequently, coral communities present in 2016 are likely to have been reorganized by both long-term community change and acclimation mechanisms. For example, less disturbed sites with cooler baseline temperatures, higher mean historical SST background variability, and infrequent extreme warm temperature stresses were associated with Acropora-dominated communities, while more disturbed sites with lower historical SST background variability and frequent acute warm stress were dominated by stress-resistant massive Porites corals. Overall, the combination of taxon-specific responses, community-level reorganization over time, geographic variation, and multiple environmental stressors suggest complex responses and a diversity of future coral communities that can help contextualize management priorities and activities.