ABSTRACT Phylogenetic studies in the eastern United States have uncovered patterns of genetic variation that suggest an influence of glacial history on various plant species. Similarly, studies have indicated regional-level genetic discontinuities corresponding with reduced gene flow between regions and populations, often associated with a geographical barrier. Here we examine the population genetics of a species found mostly in northeastern North America, but with populations at high elevations along the southern half of the Appalachian Mountains. Nine populations of the plant species Sibbaldiopsis tridentata (Rosaceae) in the eastern United States were sampled, using amplified fragment length polymorphism (AFLP) molecular markers. Levels of genetic diversity within and among populations were determined. Results indicate that the degree of intrapopulation genetic variation varies between populations. A statistically significant discontinuity is identified between populations east and west of the Valley and Ridge Province, which suggests that this region has likely acted as a barrier to historical gene flow. Within the Appalachian Mountains, northeastern populations show varying levels of genetic similarity to southeastern populations with no clear genetic signal delineating northern and southern populations. The genetic patterns discerned in this study suggest a complex species history, which should provide insight in future studies of this and other ecologically similar plant species.