Understanding species level relationships is a central goal in systematic botany; however, complexes of closely related and morphologically similar species often pose considerable challenges to that goal. The North American west is home to many notable genera that notoriously have difficult species complexes (e.g. Astragalus, Eriogonum, Penstemon). Mentzelia section Bartonia (Loasaceae), another example of a group with difficult species complexes, is a recently evolved and diverse clade that occurs across the North American west. Phylogenetic studies have resolved many relationships across Mentzelia, but the relationships within a species complex of perennial, subshrub species that occurs in the Mojave Desert, Great Basin, and Colorado Plateau remains elusive. This arid-adapted clade, which is referred to as the Mojave clade, has significant conservation implications due to three narrowly endemic species: Mentzelia polita and Mentzelia tiehmii are state listed, and Mentzelia leucophylla is federally listed. Species relationships within the Mojave clade are not fully understood. Populations of Mentzelia oreophila from California and Nevada, for example, are not monophyletic. We generated restriction site associated DNA sequence data (RADSeq) to address evolutionary relationships in the Mojave clade. Our results corroborated previous studies in continued recognition of Mentzelia polita, Mentzelia leucophylla, and Mentzelia tiehmii; however, Mentzelia oreophila was recovered in three clades that includes a California clade, a Nevada clade, and one with Mentzelia puberula. Incomplete lineage sorting and hybridization might have generated conflicting phylogenetic signal between Mentzelia oreophila and Mentzelia puberula. Increasing population level sampling will aid in species delimitation and further help to understand how gene flow and/or hybridization is influencing population level dynamics in the Mojave Desert.