Habitat fragmentation can lead to a cascade of negative effects such as reduced fitness, population decline, or extinction. Narrowly distributed species occurring in small populations across a fragmented landscape are strong candidates for conservation assessment. Small, isolated populations are more likely to be inbred and contain less genetic variation than widespread, panmictic populations. Inbreeding depression leads to loss of genetic variation and to less adaptability. Amsonia tharpii (Apocynaceae) is listed as rare and endangered by the states of New Mexico and Texas and consists of five populations occurring on limestone and gypsum substrates across the Permian Basin in eastern New Mexico and western Texas. The Permian basin is a natural resource rich region and produces more crude oil than the rest of the United States. It is suspected that land use and climate changes have led to demographic decline for all A. tharpii populations and field surveys to find seedlings have been unsuccessful. In addition, there are taxonomic uncertainties surrounding A. tharpii and A. fugatei. We generated two double digest Restriction site associated DNA sequence data (ddRADSeq) sets to address phylogenetic and population genetic questions for conservation assessment. The phylogenetic dataset was used to elucidate evolutionary relationships across the western North American Amsonia, and to determine if A. fugatei and A. tharpii are conspecifics. We then used a comparative phylogenetic framework to investigate genetic diversity, population structure, and effective population size for A. longiflora (widespread), A. fugatei (narrow endemic), and A. tharpii (threatened, narrow endemic). Phylogenetic results indicated that A. fugatei and A. tharpii are sister species to a clade containing A. tomentosa and A. arenaria. Population genetics of all three species revealed similar genetic diversities, suggesting that inbreeding and low genetic variation is not a concern for A. tharpii. However, populations of A. tharpii were found to be highly structured (K = 5) which suggests low interpopulation gene flow, genetic drift, and divergence. Flowers of Amsonia are white to blue, produce a sweet-smelling scent and nectar, open in the evening, and have elongated floral tubes. These traits are consistent with moth pollination and large bodied moths such as Hyles lineata (hawkmoths) are capable of transferring pollen long distances. Population structure for A. longiflora and A. fugatei suggest hawkmoth pollination as these were panmictic. Populations of A. fugatei are geographically closer together and are not interspersed with oil and gas wells like A. tharpii. The lack of gene flow among A. tharpii populations has created distinct population segments or ESU’s (evolutionary significant units) with unique genetic variation (and evolutionary potential). We therefore recommend that all populations of A. tharpii be treated as distinct population segments and protected.