Extensive chloroplast introgression has been documented in polyploid Betula species of eastern North America. However, the extent to which the nuclear genomes of these species are differentiated is unknown. Therefore, we evaluated genetic differentiation among largely sympatric Betula papyrifera, B. alleghaniensis, and B. lenta using nuclear microsatellite markers. Principal components analysis (PCA) and analysis of molecular variation (AMOVA) were used to evaluate genetic differentiation. Bayesian model-based clustering was used to identify putatively admixed individuals. Despite a high incidence of allele sharing, all of the species were significantly differentiated even within zones of sympatry. A number of individuals were identified as possibly admixed between B. papyrifera and B. alleghaniensis and between B. alleghaniensis and B. lenta. Admixture estimates between B. alleghaniensis and B. papyrifera increased significantly moving northward into the sympatric zone, suggesting the occurrence of hybridization in previously glaciated habitats. In contrast, admixture proportions of B. papyrifera and B. alleghaniensis did not show a significant geographic trend, which points to recent ancestry as the likely cause of allele sharing between these two species. We suggest that allele sharing of B. papyrifera and B. alleghaniensis results from a combination of ongoing gene flow and historic introgression via pollen swamping during northward colonization into post-glacial environments.