Most coral reefs differ from those visited by explorers in the 15th century and described by ecologists in the 1950s, and reports of degraded reefs and hypotheses regarding the implications of the changes abound. Tests of these hypotheses require decadal-scale ecological analyses, yet data to support these efforts remain rare. In this study, 25 yr of time-series analyses from 3 habitats in St. John, US Virgin Islands, revealed changes in coral community structure that are spatially and temporally heterogeneous, only loosely coupled with local disturbances, and equivocal in terms of the coral community structure that can be projected from the recent past. In a near-shore habitat at 7 to 9 m depth, coral cover remained ~4% between 1992 and 2011, and variation in benthic community structure was driven mostly by Agaricia. In an Orbicella annularis (formerly Montastraea annularis)-dominated habitat at 9 m depth, coral cover declined from 45% in 1987 to 7% in 2011, and varied among decades. In a second O. annularis-dominated habitat at 14 m depth, coral cover increased from 32% in 1987 to 49% in 2002, but then declined to 29% in 2011. The density of small corals also changed between 1994 and 2011, beginning with a density (colonies per 0.25 m2) of 3.5 in 1992, rising to 4.9 in 2005, but declining to 3.0 in 2011. Each genus of small corals responded in dissimilar ways over time, with genera waxing and waning in abundance on multiple occasions and in asynchronous patterns. The reefs of St. John have changed markedly since 1987, but the present results show how adjacent habitats and sympatric coral taxa translate similar environmental signals into discordant community trajectories that suggest that these coral communities will not disappear in the short term.