Cycladenia humilis (Apocynaceae) is a rare perennial herb native to western North America and has a fragmented distribution in California, Utah, and Arizona. Populations in Utah and Arizona are federally listed as threatened, while there is no conservation status applied to California populations. Using genetic (three chloroplast and two nuclear DNA loci) and morphological characters, intraspecific variation between populations of C. humilis and current taxonomic conventions were assessed. Nested Clade Phylogeographic Analysis and Bayesian phylogenies were used to assess patterns within C. humilis and supported three main population groupings: a northern California, southern California, and Colorado Plateau group. The northern California populations represent a distinct group and include populations from the Santa Lucia Mountains contrary to current classifications. The southern California group consistently includes populations in the San Gabriel and Inyo Mountains and was unique from any other region. The Colorado Plateau represents a group distinct from all other groups. The resilience of C. humilis on the Colorado Plateau to human threats remains unknown, but based on its frequency being comparable to California and our findings that considerable genetic variation exists within the species and within populations on the Colorado Plateau, we recommend that the threatened status of C. humilis be lifted.