The Chihuahuan Desert is the largest arid zone in North America and is recognized as the most important center of diversity for cacti. Coryphantha durangensis is an endemic species of the Chihuahuan Desert that is currently listed in both the IUCN and NOM-059-SEMARNAT-2010. We used microsatellite markers to analyze the diversity and genetic structure of populations of this species. Low levels of genetic diversity were found among pop-ulations, but there was genetic differentiation within individuals. The isolation analyses suggest that the pop-ulation genetic structure can be explained by isolation-by-resistance in climate and isolation-by-resistance in altitude. Poor gene flow was observed between populations, which may be due to several factors, such as climatic fluctuations that have occurred in its distribution area since the Pleistocene, the lack of known pollinators for the species, and the distribution area of this species in small discontinuous mountains that have allowed the isolation of populations, coupled with slow growth and the long time lapse between germination and the first flowering that this species presents. This is the first report on the genetic diversity and population structure of C. durangensis, and the results of the study can be used to develop and promote management and conservation strategies.