The distribution of dominant coral genera and their response to the recent sea temperature anomalies in the last three decades are analyzed across reefs of the Maldivian Archipelago, which spans 860 × 120 km in the central Indian Ocean. The Maldives suffered one of the worst coral mortality rates in the Indian Ocean in the 1998 warming event and experienced two sub-lethal thermal anomalies in 2003 and 2010. The results showed that the Acropora proved an important driver of post-1998 recovery and has become a major dominant genus in most Maldivian reefs at present. The average coral cover and proportion of acroporids have decreased from south to north and represent correspondently 70.6/59% for the southern atoll, 62/53% for the central atoll and 33/10.3% for the northernmost atoll. Stylophora, Seriatopora and the hydrocoral Millepora were not found and are considered candidates for local extirpation from the Maldives. Higher thermal variability and frequency of thermal stress might lead to the decrease in the abundance of susceptible taxa in the northernmost atoll. No phase-shift to algae-dominated reefs was observed in any of the three locations. Factors contributing to coral recovery and acclimatization are discussed.