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Effective conservation management relies upon accurate taxonomic information and an understanding of the genetic health and population structure for each species. Penstemon acaulis and P. yampaensis are endemic species to Colorado, Utah, and Wyoming, and have been considered for listing under the Endangered Species Act (ESA). There is little biological data published about either and there remains taxonomic uncertainty surrounding the two. Phylogenetic analyses showed P. acaulis and P. yampaensis to be distinct, monophyletic lineages and morphological data further supported taxonomic recognition of both species, however these results did not support the previous species boundaries. Eastern populations of P. acaulis were shown to be more closely related to P. yampaensis, and without those populations the total species range of P. acaulis decreased to a single 900 square kilometer region. Population-level analyses showed populations of P. acaulis and P. yampaensis had low levels of inbreeding despite relatively low levels of heterozygosity, indicating fair genetic health. There were three distinct genetic groups identified within P. yampaensis but only one in P. acaulis, thus it may be susceptible to biotic or abiotic changes that wouldn’t be as impactful on P. yampaensis. In order to preserve the maximum amount of genetic diversity, healthy P. acaulis populations and populations from each P. yampaensis genetic group should be targeted for protection or seed collection. With the significant decrease in actual range and expected genetic diversity, Penstemon acaulis should be reconsidered for listing under the ESA, pending further demographic and occurrence monitoring.