The distribution of Pyganodon grandis (Say, 1829) and the entire community of unionid freshwater mussels within the Laurentian Great Lakes became greatly reduced following invasion of dreissenid mussels. While some populations remain, how much gene flow still occurs is not known, nor has the level of population structure been examined within a large lake subsequent to dreissenid infestation. Pyganodon grandis is a common and relatively abundant lacustrine species that utilizes diverse host fish, and, therefore, it may disperse as much as or more than any other unionid species in the region. To test for population structure, we examined a fragment of the maternal mtDNA COI gene from 300 individuals encompassing shallow areas from Lake Erie's western and central basins, Sandusky Bay, Lake St. Clair, and the upper Niagara River. Another 94 individuals from the upper Great Lakes and upper Mississippi River watersheds were added to the analysis. A total of 34 different haplotypes were found for P. grandis in the Lake Erie watershed, but just one was common and composed > 80% of all individuals. No other haplotype exceeded a frequency of 2% and most were found only once. Just thirteen haplotypes were found west of Lake Erie, and only the common haplotype and one other were shared with the Lake Erie watershed. However, structure in haplotype frequencies and the presence of one very different clade were limited to samples abutting the Red River of the North. Thus recent population declines in Lake Erie appear not to have significantly impacted levels of genetic variation.