Discovering the extent of genetic differentiation between closely related taxa facilitates decisions regarding species protection under the Endangered Species Act. Here, we analyze genotype data to explore the relatedness of two buckwheat species: Eriogonum soredium, a narrow endemic under consideration for protection, and a widespread close relative, Eriogonum shockleyi. Eriogonum soredium grows only on Ordovician limestone outcroppings in west central Utah, whereas the range of E. shockleyi is broad, spanning the western United States from Colorado to California, and Idaho to Arizona. Eriogonum shockleyi is suspected of hybridizing with other buckwheats throughout this range. We detected higher levels of genetic diversity in E. shockleyi than in E. soredium, supporting the hypothesis that E. soredium is a derivative of E. shockleyi. We found moderate levels of admixture between the two taxa, implying the presence of incomplete reproductive barriers. Analysis of population structure revealed a genetic distinction between the two species. We found that genetic distance between samples is influenced more by taxon designation than geographic distance. Genetic evidence supports continued treatment of E. soredium as a distinct evolutionary entity.