The Chihuahuan Desert includes many endemic angiosperm species, some having very restricted geographic ranges. One of these species is Oreocarya crassipes (I. M. Johnst.) Hasenstab & M. G. Simpson, an endangered distylous gypsophile from the Trans-Pecos region in southern Brewster County, Texas, USA. The species is known from 10 populations, and this small number of populations, human development in the area, a distylous breeding system, and edaphic requirements threaten the long-term viability of the species. Using both hundreds of single nucleotide polymorphisms identified via tunable genotyping-by-sequencing (tGBS) and 10 microsatellite loci, patterns of genetic diversity, demography, selection, and migration were examined for 192 individuals from four populations of O. crassipes. From the sampled individuals, two populations (clusters) were identified via multiple methodologies and with both types of data. With SNP data, population substructure was further resolved among one of these populations to identify two distinct groups of individuals. Multiple individuals recognized as having mixed ancestry, along with Fst values and AMOVA results, provide evidence of genetic exchange among populations, which is less common for gypsophiles than non-gypsophiles, and the rate of migration among populations has been increasing recently. The Fst values for O. crassipes are more similar to those of other rare species than to other gypsophiles. Additionally, while distyly specifically does not necessarily impact the population genetics of the species, allogamy, which is facilitated by distyly, seems to have played a role in the genetic structure of O. crassipes.