Coral reefs have been threatened by various human and natural environmental disturbances, especially by widespread water temperature increases in 1997/1998. To understand the recovery of coral communities and shifts in their species compositions, long-term monitoring at the same location is important. Previously, we reported changes in the dominant taxa in a coral community before and after bleaching in 1998 at Shiraho Reef in the southern Ryukyus, Japan. In the present study, we continued monitoring the site for 15 yr to quantify how the coral community changed temporally and spatially. We used transect surveys and time-series aerial photographs and analysed the data with reference to seawater temperature and typhoon records. Net coral area along the transect lines increased from 1998 to 2003, but then decreased by 2008 mostly due to a decline in branching Montipora spp. The resulting net coral area was lower in 2012 than it was before the 1998 bleaching event. Aerial photographs also showed that the coral area at Shiraho Reef was similar between 1995 and 2000, but declined afterward. This decrease resulted from multiple disturbances, including bleaching events in 1998 and 2007, physical damage by 5 consecutive strong typhoons and likely inputs of sediments from heavy rain. Coral taxa reacted differently to the environmental stresses. The main change observed was a shift in the dominant taxa from branching Montipora and Acropora to Heliopora coerulea and massive and branching Porites. Those species have persisted due to high recruitment rates in H. coerulea and/or their tolerance to disturbances such as high thermal stresses, sedimentation and physical damage by typhoons.