Climate change is a major threat to coral reef ecosystems worldwide. A key determinant of the fate of reef corals in a warming climate is their capacity to tolerate increasing thermal stress. Here, an increase in thermal tolerance is demonstrated for three major coral genera (Acropora, Pocillopora and Porites) following the extensive mass bleaching event that occurred on the Great Barrier Reef (Australia) in 1998. During the subsequent and more severe thermal stress event in 2002, bleaching severity was 30–100% lower than predicted from the relationship between severity and thermal stress in 1998, despite higher solar irradiances during the 2002 thermal event. Coral genera most susceptible to thermal stress (Pocillopora and Acropora) showed the greatest increase in tolerance. Although bleaching was severe in 1998, whole-colony mortality was low at most study sites. Therefore, observed increases in thermal tolerance cannot be explained by selective mortality alone, suggesting a capacity for acclimatization or adaptation. Although the vulnerability of coral reefs remains largely dependent on the rate and extent of climate change, such increase in thermal tolerance may delay the onset of mass coral mortalities in time for the implementation of low-emission scenarios and effective management.