Benthic assemblages associated with pen shells (Pelecypoda: Pinnidae) in a Holocene back-barrier marine environment and in an exposure of Mississippian rocks that are inferred to be back-barrier marine deposits, appear to have more structural similarities than differences, despite their separation by over 300 million years and dominance by organisms that are not closely related taxonomically. Both of the studied assemblages occur in fine-grained, calcareous siliciclastic deposits. Excluding the pen shells, each assemblage is dominated by three species, all of which are epibenthic suspension feeders in the Mississippian association, while two of the three are epibenthic suspension feeders in the Holocene association. However, the Mississippian dominants are free-lying or byssally attached, while one of the two epibenthic dominants in the Holocene association is cemented (Crassostrea) and the other is an intermittent swimmer (Aequipecten). The Holocene assemblage has a substantially higher proportion of shallow burrowers than did the Mississippian assemblage, which may be a contributing cause of the differences in life habits of the dominant species, inasmuch as mobile and cemented epibenthic organisms are less likely to be disturbed by churning of surficial sediment by shallow burrowers than are free-lying organisms. Within the Holocene study site, pen shells are found only in marine grass beds. The Mississippian pen shells are associated with a conspicuously increased abundance of erect bryozoan fragments and also with a higher species richness than associated beds within the measured stratigraphic section. It is inferred that the erect bryozoans baffled currents, thereby reducing flow velocity and increasing the availability of microenvironments, in much the same way as modern sea-grass patches that contain pen shells.