The hickory shad (Alosa mediocris) is a relatively understudied species of the anadromous fish sub-family Alosinae. This study, the first population genetic analysis of this species, employed 12 neutral microsatellite loci to estimate genetic diversity and population structure in tributaries of lower Chesapeake Bay, Virginia including James River and its tributaries (Appomattox and Chickahominy Rivers), Rappahannock River, and Pamunkey River. Genetic variation was extremely low. Estimates of observed heterozygosity were lower than expected heterozygosity. Significant population structure was detected among the six samples (FST = 0.093, p = 0.01). Effective population sizes were low (Ne ranged from 2 to 134). The lack of genetic diversity, especially compared to that of the American shad, was striking and could be the result of a bottleneck that took place more than thirty years ago which may plausibly account for the low genetic variation observed across all populations.