Glossopetalon inhabits arid regions in the American west and northern Mexico on limestone substrates. The genus comprises four species: G. clokeyi, G. pungens, G. texense, and G. spinescens. Three of the species are narrow endemics. The fourth, G. spinescens, is a widespread species with six recognized varieties. All six varieties are intricately branched shrubs that have been difficult to identify due to a lack of clearly delineating morphological characters. Characters typically used to differentiate the varieties of G. spinescens, such as stem coloration, leaf blade size, and presence of stipules, are highly variable within and among populations. A custom protocol of double digest restriction-site associated DNA sequencing (ddRAD) was used to resolve the phylogeny of Glossopetalon and address if population genetic data analyses (such as STRUCTURE, SVDquartets, and phylogenetic networks) support the recognition of six varieties of G. spinescens. Glossopetalon was fully supported as monophyletic and G. pungens was resolved sister to the remaining taxa in the genus. The varieties of G. spinescens were resolved as two distinct lineages corresponding to their biogeography, one to the northwest (lineage 1) and one to southeast (lineage 2) of the species range. Glossopetalon clokeyi was resolved at the base of lineage 1 and G. texense was embedded within lineage 2 sister to G. spinescens var. spinescens. Taxonomic changes include the recognition of G. texense and G. clokeyi as varieties of G. spinescens and description of a unique population from northern Arizona as a new variety, G. spinescens var. goodwinii.