Premise: Previously published evidence suggests that Draba maguirei, a mustard endemic to a few localities in the Bear River, Wellsville, and Wasatch Mountains of northern Utah, may represent a cryptic species complex rather than a single species. Conservation concerns prompted an in-depth systematic study of this taxon and its putative relatives. Methods: Sampling most known populations of D. maguirei s.l. (D. maguirei var. maguirei and D. maguirei var. burkei), we integrate data from geography, ecology, morphology, cytogenetics and pollen, enzyme electrophoresis, and the phylogenetic analysis of nuclear internal transcribed spacer sequences to explore potential taxonomic diversity in the species complex. Results: Draba maguirei var. burkei is shown here to be a distinct species (D. burkei) most closely related to D. globosa, rather than to D. maguirei. Within D. maguirei s.s., the northern (high elevation) and southern (low elevation) population clusters are genetically isolated and morphologically distinguishable, leading to the recognition here of the southern taxon as D. maguirei subsp. stonei. Conclusions: Our study reveals that plants traditionally assigned to D. maguirei comprise three genetically divergent lineages (D. burkei and two newly recognized subspecies of D. maguirei), each exhibiting a different chromosome number and occupying a discrete portion of the geographic range. Although previously overlooked and underappreciated taxonomically, the three taxa are morphologically recognizable based on the distribution and types of trichomes present on the leaves, stems, and fruit. Our clarification of the diversity and distribution of these taxa provides an improved framework for conservation efforts.