Taxonomic delimitation of rare species is vital for accurate assessments of diversity and for their conservation. Cycladenia humilis, the sole species of Cycladenia, is an enigmatic perennial widely dispersed across the western United States. Within this species there are three currently recognized varieties: C. humilis var. humilis in Northern California, C. humilis var. venusta in Southern California, and C. humilis var. jonesii in Utah and Northern Arizona. Some populations occur geographically in areas between the typical distribution of each variety and the presently accepted taxonomy inadequately addresses these populations. Using five nDNA regions, we seek to clarify relationships between current varieties and assess the pattern of variation throughout the species. Analyses including K-means clustering, principle component analysis, fields for recombination, AMOVA, and ecological niche modeling were applied. Results indicate significant genetic structure between varieties and supports recognition of C. jonesii at the species level as distinct from C. humilis. Well defined intraspecific groupings are evident in the data, with evidence supporting the recognition of an additional variety in C. humilis, and two varieties in C. jonesii. Haplotype diversity and relationships between metapopulation clusters inform conservation efforts regarding diversity within Cycladenia and offer insights into the historical demography of this genus.