The atolls and coral banks of the Chagos Archipelago (British Indian Ocean Territory) in the central Indian Ocean were severely affected by the El Niño Southern Oscillation (ENSO) thermal event that started in 2015 and which lasted for nearly two years. On these reefs, coral mortality reduced scleractinian coral cover from 40-50% to <10% and commonly to only about 5% in water less than 15 m depth. The 3-dimensional structure of the reefs was significantly reduced as a result, and the prolonged warming almost eliminated soft corals. Most atolls of the archipelago are uninhabited, so any changes are driven by broad environmental changes rather than by direct, local anthropogenic effects. Coral cover was first measured in 1978, temperature loggers have recorded water temperature at various depths for the last 11 years, and the results of the recent warming event are placed in this context. Over this time, cover has declined severely along with a general rise in water temperature of one third of a degree on ocean reefs and by over one half of a degree in lagoons. Major fluctuations of coral cover caused by warm episodes have sometimes but not always coincided with ENSO events and have occurred on top of the increasing trend in background temperatures. Juvenile coral populations have also recently severely declined following the mortality of the adults. Estimates of calcification suggest a marked reduction, from a state of vigorous reef growth that had not long recovered from the earlier severe warming event of 1998, to a state of net erosion. Predictions suggest that recurrences of mass mortalities will take place too frequently for any significant recovery of reef health in these atolls by the late 2020s.