The key to predicting the possible response(s) of coral reefs to hypothesized future global warming is the knowledge of their response(s) to previous extreme climatic events. We obtained 80 high-precision U/Th ages for 78 dead massive Porites colonies from the Nansha Islands, South China Sea, with an aim to understand the long-term history, frequency, timing and causes of local coral mortality. Our results reveal a number of significant episodes of coral mortality since 1860 AD, with an apparent increase in frequency and severity since 1930 AD, and more recently since 1970, especially when only synchronized mortality events found to have occurred on both reefs were compared. The synchronized mortality events centered around 1865–1875, 1895–1900, 1910–1920, 1930–1945, 1970–1985 and 1990–2005 AD, which imply regional common causes, were found to correlate well with the warm phases of the El Niño Southern Oscillation (ENSO) (i.e. El Niño years, e.g. some recent ones during 1972–1973, 1982–1983, 1991–1994, 1997–1998 AD) on inter-annual time scale, as well as with positive phases of the Pacific Decadal Oscillation (PDO) or its sharp phase transitions on inter-decadal time scale. Synchronized coral mortality was absent during prolonged negative PDO phases, e.g. during 1950–1970 AD. Overall, the data shows that immediately before, and at the time of, modern local ecological monitoring, the region's coral communities had already experienced several recent episodes of stress. The increased frequency distribution of mortality ages since 1930 AD and more recently since 1970 AD appears to coincide with progressively warmer sea-surface temperatures, both regionally and globally. Our data highlight the vulnerability of local coral communities in the face of present and predicted future warming.