Assessing genetic variation in species of conservation concern is critical for developing sound recovery strategies. In this study, we compared sympatric populations of two related species, the endangered Quadrula fragosa (Conrad, 1836) and its common relative Amphinaias pustulosa (Lea, 1831), using standard genetic parameters such as allelic richness, heterozygosity, and effective population size. Our primary aim was to determine if a small population size and isolation from conspecifics had negatively affected the genetic diversity of this population of Q. fragosa. By comparing the endangered species to a related and sympatric, common species we can assess the rare species for genetic effects associated with reduced population size, and in addition, develop management targets for what a recovered Q. fragosa population looks like genetically. Examination of eight microsatellite loci indicated that Quadrula fragosa exhibited reduced genetic variation when compared to A. pustulosa at all measures, however, no evidence of a genetic bottleneck or inbreeding was discovered for either species. A comparison of known fish hosts and reproductive period for these two species point to competition for fish hosts as one possible explanation for the smaller population size of Q. fragosa. We discuss the implications of our findings for the conservation and management of freshwater mussels.