The authors tested whether various measures of DNA variation between Hudson River populations and adjacent populations of Atlantic sturgeon (Acipenser oxyrinchus), American shad (Alosa sapidissima), and striped bass (Morone saxatilis) were sufficient to discriminate among their conspecific populations. American shad populations surveyed for mtDNA variation were highly diverse genotypically, but genotypic frequencies among the populations of the Connecticut, Hudson, and Delaware rivers were statistically homogeneous. In contrast, Atlantic sturgeon and striped bass populations of the Hudson River were not genotypically diverse, but they were differentiated from northern and southern populations.