Caribbean coastal ecosystems have undergone severe degradation both historically and recently, primarily caused by the synergistic effects of overfishing, eutrophication, sedimentation, disease, and other factors associated with humans. Baseline conditions from pristine Caribbean reefs and seagrass beds are required to understand and quantify degradation. Only the fossil record can provide pre-human baselines. We present preliminary results from a recently discovered mid-Holocene (7.2-5.7 ka) fossil fringing reef and seagrass system in Bocas del Toro, Panama. Molluscan assemblages from the fossil reef and seagrass habitats were compared to death assemblages in corresponding modern habitats. The proportion of suspension-feeding molluscs more than doubled from fossil to the present day in the reef habitat, and the proportion of herbivores declined by a third, reflecting declines in coral cover and architecture, and increased eutrophy. Conversely, in seagrass beds, the proportion of different mollusc guilds was remarkably similar between fossil and modern day, suggesting that unlike reefs, seagrass beds are functionally similar today compared to a "pristine" baseline, although key community members were different. Our study reveals novel evidence that the health of molluscan communities on Caribbean reefs may have declined to the extent observed in corals and fish, and that the decline follows a trajectory predicted by known ecosystem degradation. Molluscs represent a biodiverse and functionally crucial component of reefs and must be considered in ecosystem-scale research on reef conservation. Revealing the structure of baseline communities using the fossil record represents one important step toward this aim.