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Severe bleaching events caused by marine heat waves over the past four decades have now affected almost every coral reef ecosystem in the world. These recurring events have led to major losses of coral cover, with adverse consequences for tropical reef ecosystems and the people who depend on them. Here, we document two consecutive and widespread coral bleaching events on remote atolls in the Coral Sea in 2016 and 2017. In each year, the proportion of colonies that bleached was strongly related to heat exposure (measured as degree heating weeks, DHW, degrees C-weeks), depth and coral assemblage structure. Bleaching was more severe at higher DHW exposure and at sites with a higher proportion of susceptible taxa. Bleaching was also lower at 6 m than at 2 m depth. Despite the severe bleaching in 2016 on reefs in the central section of the Coral Sea Marine Park, total coral cover was not significantly reduced by 2017, suggesting that most bleached corals survived. Moreover, bleaching was less severe in 2017 despite a higher exposure to heat stress. These results indicate that while the isolation of these oceanic reefs provides no refuge from bleaching, low nutrient levels, high wave energy and proximity to cooler deeper waters may make coral on these reefs more resistant to bleaching-induced mortality.