Hybridization in plants can be common, may lead to increased genetic variation, and in some instances the formation of new species. For endangered species, hybridization can introduce novel genetic variation and potentially increase genetic diversity. In contrast, hybridization can negatively affect an endangered species or population by introducing maladaptive alleles into locally adapted lineages or lead to the homogenization of once distinct lineages. We used microsatellites, AFLP markers, and morphological data to identify potential hybridization between the endangered Roan Mountain bluet (Houstonia purpurea var. montana) and its commonly occurring congener (H. purpurea var. purpurea). We used these data to clarify the taxonomic relationship of these varieties and to assess population structuring of the Roan Mountain bluet. The results showed that these lineages are distinct and few individuals exhibited admixture in several populations. Additionally, the results showed there is genetic population structure among the remaining populations of H. purpurea var. montana, which is consistent with other mountaintop species. Our results show that Roan Mountain bluet populations should be protected to maintain genetic diversity and monitored to assess future hybridization, and additional studies that comprise a greater population sampling would provide more information.