The benthic community structure of the shallow reefs of St. John, US Virgin Islands, was studied from 1992 to 2007 to test the hypotheses that the abundances of non-scleractinian invertebrates have changed, and further, that the changes are associated with variation in the percentage cover of scleractinian coral and macroalgae. The study utilized photoquadrats (0.25 m2) from fringing reefs (7–9 m depth) characterized by igneous boulders and low (b5%) coral cover, and results from six sites were pooled to describe these reefs as a single habitat. Photoquadrats were analyzed biennially for the abundance of invertebrates, particularly those belonging to four well represented classes (Anthozoa, Demospongiae, Echinoidea, and Polychaeta), as well as the cover of scleractinians and macroalgae. Overall, the combined (multivariate) abundance of 30 invertebrate taxa changed over time, the combined (multivariate) abundance of the four invertebrate classes changed over time, and the individual (univariate) abundance of anthozoans, sponges, and echinoids changed over time. Throughout the study, coral cover remained b5%, and while it varied significantly, it did not display a consistent trajectory of change; in contrast, the cover of macroalgae increased throughout the study. While it is unsurprising that the abundances of invertebrates changed over 15 y, notably they varied even though coral cover remained stable, in only a few cases were they related positively to macroalgal cover, and in most cases it was members of the suspension feeding guild that became more abundant. These outcomes suggest that: (1) benthic invertebrates on the shallow reefs of St. John may be more strongly influenced by regional (e.g., larva supply) than local (e.g., coral cover)conditions, (2) Caribbean reefs have changed more since the early 1990s than can be inferred from variation in cover of coral and macroalgae, and (3) suspension feeding invertebrates have become more common on shallow fringing reefs in at least one location.