Background: Over the relatively short period of its evolutionary history, Boechera (Brassicaceae) has undergone rapid radiation that has produced 70+ morphologically distinct, sexual diploids. However, reproductive isolation has moved more slowly than morphological divergence in this group and the diploids appear to hybridize frequently where they coexist. Boechera duchesnensis appears to be the result of hybridization between its putative parents Boechera thompsonii and Boechera formosa. Objectives: The objectives of this study are to (i) analyze and document genetic diversity patterns in the population structure, - including allelic and heterozygosity frequencies - of B. thompsonii and B. formosa in concert with their geographic distribution to determine clustering relationships within these populations, (ii) confirm and expand the morphological characteristics of B. thompsonii and B. formosa, as initially proposed in the literature, including pollen and trichome structure using Scanning Electron Microscopy (SEM) to confirm ploidy level and to determine whether both putative parent species share morphological characteristics with their apomictic diploid offspring, and (iii) use genetic and morphologic evidence to show that B. thompsoii and B. formosa are, in fact, the parents of B. duchesnensis by comparing the genetic diversity patterns, population structure, and morphological characteristics of B. duchesnensis, to those of its proposed putative parents (B. thompsonii and B. formosa) and to confirm that B. duchesnensis shares characteristics of Boechera. Methods: Microsatellite data from 14 loci previously identified in Boechera were used to reexamine the current classifications and taxonomic foundations of three Boechera spp. GenAlEx 6.501 (Peakall and Smouse, 2006, 2012) was used to analyze genetic population structures of two divergent sexual diploids in the genus Boechera: B. thompsonii and B. formosa and to later compare those with the population structure of B. duchesnensis. Geographicaldata were plotted using ArcGIS 10.1 (Esri, 2012) to map heterozygosity distribution. Cluster analysis was run with STRUCTURE 2.3.3 (Pritchard et al., 2000; Falush et al., 2003, 2007) and distribution of allelic diversity and heterozygosity was subsequently compared within each taxon and correlated with geographic distribution characteristics. Resultant data were then compared with B. duchesnensis data to document genetic diversity patterns, population structure, and morphological characteristics. Key Results: Analysis of genetic diversity patterns, allelic distribution of the populations, and heterozygosity of B. thompsonii and B. formosa across their geographic range identified four genetically distinct clusters within B. thompsonii, and one genetically distinct cluster in B. formosa. Allelic frequencies in all four discrete population clusters of B. thompsonii and in one discrete population cluster of B. formosa were close to values found in species on the decline. Reproductive isolation, genetic variability, and allelic frequencies were determined, specimen elevations reported, and morphological characteristics reported in the literature were confirmed and expanded. A codominant genetic analysis performed for 14 different loci for B. duchesnensis against those of its parents showed that B. duchesnensis inherits alleles from both putative parents and confirms B. thompsonii and B. formosa as the parents of B. duchesnensis. Observed levels of heterozygosity of B. thompsonii and B. formosa were lower than expected levels and lower than those of other outcrossing diploids. The mean overall observed heterozygosities for each cluster were determined and documented by geographic location. A substantially higher level of observed heterozygosity in B. duchesnensis (Ho = 0.908) consistent with genetic fixation of a heterozygote and apomixis, supports hybridization as a speciation mechanism and apomixis as a mode of reproduction accounting for genotypic and phenotypic diversity. Morphological characteristics, especially those of pollen and trichomes were confirmed, expanded, and documented with SEM imagery. Discussion: This study provides an analysis of the genetic diversity patterns inherent in the population structure, allelic frequencies, allelic variation among individuals of the rare sexual diploids B. thompsonii, B. formosa, and the apomictic diploid B. duchesnensis in correlation with their geographic distribution. There is an implication of a reproductive barrier, within populations of the same species, that contributes to genetic isolation between clusters. I analyze the tendency of reduced heterozygosity to lead to genetic fixation, reproductive isolation, and how the heightened heterozygosity supports the classification of B. duchesnensis as an apomict. Assessing potential populations that might exist based on similar characteristics could possibly provide inferences about where future research might find similar examples of this hybridization. Reproductive isolation is hypothesized to limit gene flow between identified clusters of B. thompsonii and B. formosa exacerbating low observed heterozygosity levels and low allelic frequency levels. Population studies and cluster analysis have implications for offering future conservation strategies for both taxa.