Invasive species are one of most significant factors in human-influenced global change. Management actions that prevent the spread and impacts of invasive species require knowledge of their ecological and genetic characteristics. The genetic characteristics of the invasive wine raspberry, Rubus phoenicolasius Maxim. (Rosaceae) and the native sawtooth blackberry, Rubus argutus Link, were examined in two forest habitats on the Maryland Coastal Plain. Using inter-simple sequence repeat (ISSR) markers we quantified the genetic diversity of both species. We analyzed genetic diversity using analysis of molecular variance (AMOVA) and found less genetic diversity in the invasive species, R. phoenicolasius, with variation between sites was 0.418 between sites and 0.075 within sites as compared to the native, R. argutus, where the variation between sites was 1.538 and 0.370 within sites. The lower genetic diversity in the invasive may be due to a history of limited introductions or frequent self-fertilization and clonal reproduction.