Anticlea vaginata (Melanthiaceae) is a rare and endemic plant species restricted to hanging gardens in low-elevation desert regions of the Colorado Plateau. Its more widespread congener, A. elegans, is morphologically similar, but occurs in montane forests that encompass and extend beyond the natural range of A. vaginata. Here, we use morphometric and genetic analyses to investigate the biogeographic origin, population structure, and taxonomic classification of A. vaginata relative to A. elegans. Our results demonstrate that A. vaginata is closely related to and morphologically indistinguishable from A. elegans and likely represents remnant populations of A. elegans derived from a Pleistocene vicariance event. We conclude that A. vaginata warrants treatment as Anticlea elegans subsp. vaginata, since it exhibits a similar level of differentiation from A. elegans subsp. elegans as subsp. glaucus. Since A. vaginata occupies an ecologically unique niche, exhibits a distinct flowering period and harbors unique alleles, we suggest separate conservation management in order to protect this subspecies and its fragile habitat, which is currently threatened by climate change and the potential for groundwater development.