Delimiting communities in marine habitats is difficult because co-occurring species often have different life histories and the life stages experience the environment at different spatial scales. The habitat of a particular community is embedded within a larger habitat or ecosystem with many species shared between the focal community and the larger system. Pen shells (Atrina rigida) are large bivalves that, once the mollusk dies, provide shelter for motile species and hard substrate for settling larval invertebrates and egg-laying fishes. In St. Joseph's Bay, Florida (29°45′N, 85°15′W), pen shells are the most abundant source of hard substrate, especially inside sea grass (Thalassia testudinum) beds, where they reach densities of 0.1-4.0 m -2. This study, which was conducted from May to August 2005, measured the overlap in species densities between dead pen shells and the surrounding sea grass communities at eight sites to determine the discreteness of the pen shell communities. Of the 70-epibenthic taxa recorded, 66% were found on the pen shells but not in the surrounding sea grass habitat. Community structure, which varied among shells within sites and among the eight sites, could be related to sea grass characteristics such as blade density and length either directly (e.g., inhabitants of pen shells directly benefit from the surrounding sea grass) or indirectly (e.g., pen shells and sea grass both benefit from similar factors such as current and nutrients). Pen shells were randomly distributed at several spatial scales within the 15 x 15 m sites as were many motile species. Two exceptions were the shrimp, Palaemon floridanus and the amphipod, Dulichella appendiculata, whose distributions were clumped. Most of the sessile species had clumped distributions, tending to be very abundant when they were present. These pen shell communities provide an opportunity for experimental studies of factors affecting species diversity on small, discrete, naturally occurring habitats.