This study provides a spatial context to a temporal analysis of community structure on shallow reefs along the south shore of St. John, US Virgin Islands. By focusing on 12 to 14 sites stratified by depth (similar to 10 m) and distributed along the shores of St. John and St. Thomas, surveys in 2011 were used to explore scale-dependency in coral reef community structure by testing for effects of islands, shores (north versus south), and interactions between these 2 factors. Reefs were censused using photoquadrats that were analyzed for percentage cover, first by functional groups (coral, macroalgae, and a combined category [CTB] of crustose coralline algae, algal turf, and bare space) and then by coral genus. Multivariate analyses revealed no differences in coral reef community structure between islands or shores, although reefs differed among sites. Univariate analyses by functional group also revealed differences among sites and 1.9-fold higher coral cover around St. Thomas compared to St. John; there were no differences between shores. The common coral genera displayed unique patterns of variation among sites, with the cover of Orbicella, Montastraea, Porites, and Agaricia differing among sites but not between islands or shores, and the cover of Siderastrea differing between islands in a pattern that varied between shores. Overall, variation among sites in coral reef community structure that overwhelmed differences between islands and shores focuses attention on the importance of testing for mechanisms creating variation at this spatial scale. The present results suggest that priority effects in community succession may represent one mechanism worthy of investigation.