The conversion of grasslands to agriculture land has made the tall grass prairie one of the world’s most endangered ecosystems and has played a key role in the decline of one particular species of rare endangered orchid, Platanthera praeclara (western prairie fringed orchid, WPFO). Loss of genetic diversity, accumulation of mutations, and inbreeding all increase the risk of extinction in endangered species. Through the use of microsatellite markers to characterize allele frequencies in six populations of WPFO, evidence of inbreeding was common and highest at the most extreme northern, southern and eastern populations. Thus, suggesting that in addition to the current conservation objectives, interventions to reduce levels of inbreeding should be an additional conservation objective. The populations that warrant the greatest effort in recovery are the populations located at the edges of the range, where plants are the most likely to experience an extinction vortex.