Sponges are an ecologically important component of modern Caribbean coral reefs. However, little is known about the structure of sponge communities prior to the large-scale degradation of Caribbean reef ecosystems. Here we explore changes in the sponge community over the past millennium by analyzing the composition of sponge spicules from a sediment core collected from a lagoonal reef within the archipelago of Bocas del Toro, Caribbean Panama. The analysis reveals a change in spicule composition that began approximately 400 yr ago. During this time, the share of monaxial spicules, belonging mostly to haplosclerid and axinellid sponges, decreased while the relative number of spherical spicules, found typically in Placospongia, Geodia, and some chondrillids, increased. These results were compared with previously published data on parrotfish, corals, and reef accretion rates obtained from the same core. The increased share of spherical spicules did not correlate with contemporaneous declines in the abundance of parrotfish (determined from fish teeth) or with trends in the relative abundance of dominant coral species (determined from coral skeletal remains) but was weakly correlated with reef accretion rates (determined from sediment accumulation rates). Spicule morphogroup diversity and evenness increased over the past ~400 yr, suggesting community changes were not due to reef environments becoming less habitable for reef sponges. Although not tested directly, the increase in spherical spicules may be due to declines in the abundance of sea turtles that preferentially feed on sponges that contain these spicule types.