In this study, the abundance of Millepora spp. on the shallow (< 9-m depth) fringing reefs of St. John, US Virgin Islands, was measured from 1992 to 2008 using photoquadrats recorded annually. The objectives were to describe how a rare, yet ecologically important invertebrate has changed in abundance over 16 years, and evaluate the extent to which the changes were associated with seawater temperature and storm intensity. Millepora spp. covered ≤1.5% of the benthos throughout the study, but it increased in cover as much as 306% between some consecutive years, while decreasing 67% between other years. Overall, mean Millepora spp. cover declined 49% from 0.99±0.33% in 1992 to 0.51±0.15% in 2008, in part because colonies became 47% smaller through shrinkage and fission. The percentage cover, number of branches, and population density (i.e., colonies m−2) of Millepora spp. decreased in years characterized by warm seawater and intense storm effects, but the size of Millepora spp. colonies increased in years characterized by large numbers of cold days. Changing abundances of scleractinian corals are well documented on coral reefs, but the present study is unusual in demonstrating strong temporal variation in abundance of a rare taxon, probably as a result of some of the same physical conditions affecting scleractinians. As scleractinian corals decline in abundance, the dynamics of rare taxa are likely to play increasingly important roles in the community structure and function of tropical reefs.