Ecological theory predicts that species turnover among communities (e.g. β-diversity) and genetic turnover among populations within species (e.g. ) should be positively correlated if similar processes influence colonization and occupancy of species and gene flow and genetic drift of populations within a metacommunity. Using recently published population genomic data from multiple populations of 15 freshwater mussel (Unionidae) species across seven rivers in the Mobile and Tennessee River basins of the south-eastern USA, we conducted novel analyses examining the relationship between taxonomic turnover (β-diversity) among communities and genetic differentiation () within these species. and β-diversity were both hierarchically structured, and strong basin effects and isolation-by-distance were observed for β-diversity and for among populations within most species. Furthermore, β-diversity and were directly correlated for the overall community and among sites for individual species, indicating that factors shaping turnover among mussel assemblages are similar at the species and genetic levels. The widespread associations between turnover metrics at the community and population genetic levels of biological organization suggest that parallel processes govern species composition and intraspecific connectivity in freshwater mussel metacommunities.