Coral reefs are biodiverse ecosystems structured by abiotic and biotic factors operating across many spatial scales. Regional-scale interactions between climate change, biogeography and fisheries management remain poorly understood. Here, we evaluated large-scale patterns of coral communities in the western Indian Ocean after a major coral bleaching event in 1998. We surveyed 291 coral reef sites in 11 countries and over 30° of latitude between 2004 and 2011 to evaluate variations in coral communities post 1998 across gradients in latitude, mainland-island geography and fisheries management. We used linear mixed-effect hierarchical models to assess total coral cover, the abundance of four major coral families (acroporids, faviids, pocilloporids and poritiids), coral genus richness and diversity, and the bleaching susceptibility of the coral communities. We found strong latitudinal and geographic gradients in coral community structure and composition that supports the presence of a high coral cover and diversity area that harbours temperature-sensitive taxa in the northern Mozambique Channel between Tanzania, northern Mozambique and northern Madagascar. Coral communities in the more northern latitudes of Kenya, Seychelles and the Maldives were generally composed of fewer bleaching-tolerant coral taxa and with reduced richness and diversity. There was also evidence for continued declines in the abundance of temperature-sensitive taxa and community change after 2004. While there are limitations of our regional dataset in terms of spatial and temporal replication, these patterns suggest that large-scale interactions between biogeographic factors and strong temperature anomalies influence coral communities while smaller-scale factors, such as the effect of fisheries closures, were weak. The northern Mozambique Channel, while not immune to temperature disturbances, shows continued signs of resistance to climate disturbances and remains a priority for future regional conservation and management actions.