New molecular and ecological data have necessitated taxonomic revisions of several species complexes within Polemonium (Polemoniaceae), including P. foliosissimum, an herbaceous perennial widespread in the Intermountain West of the United States. As currently circumscribed, P. foliosissimum is a highly polymorphic species of four taxonomic varieties. One of the most striking morphological traits of the species is its diversity in flower color, which is unusual for the genus. Several species have been proposed based on this variation in flower color. However, these names have been treated as infraspecific taxa because previous authors have concluded that the presence of micropollen grains throughout the geographic range of the species complex indicated partial hybrid sterility and therefore incomplete barriers to gene flow. However, recent evidence suggests that micropollen is instead due to a gynodioecious breeding system. Using 128 nuclear loci and eight quantitative morphological traits, I clarify relationships and taxonomy within the species complex. I show that what is currently circumscribed as four varieties of P. foliosissimum represent five species that, in addition to differing in corolla color, differ in leaflet number, corolla size, and vegetative and floral pubescence. I propose a new species endemic to the White Mountains of southeastern Arizona, Polemonium apachianum. This study provides a new phylogenetic context and taxonomic circumscription to serve as a framework for future research on the evolution of floral color and sexual systems in a previously misunderstood but evolutionarily exciting system.