Cirsium ownbeyi is a habitat-specific, endemic, polycarpic thistle in northwest Colorado, northeast Utah, and southwest Wyoming. In 1998, seven C. ownbeyi populations, which ranged from 4 to >30,000 plants, were known from Wyoming. The population genetics of C. ownbeyi and the threat posed by an exotic flower head–feeding weevil, Rhinocyllus conicus, in Wyoming are unknown. Between 2014 and 2016, we visited Wyoming C. ownbeyi populations to determine (1) changes in population sizes since 1998, (2) extent of R. conicus use, and (3) amount and distribution of genetic variation within and between populations. We quantified densities of plants within populations by life stage, population spatial extents, and, for 10 plants per population, proportion of flower heads with R. conicus ovipositions. Data at 6 simple sequence repeat loci were also collected. Three C. ownbeyi populations were <10% of their 1998 estimated size, 3 populations were unchanged, and one population was substantially larger than in 1998. We found Rhinocyllus conicus oviposition in all Wyoming C. ownbeyi populations, and we interpret increasing use by this weevil over our monitoring period as indicating recent colonization. Low FST and FIS values suggest that levels of C. ownbeyi inbreeding were low and that there was considerable gene flow among populations. Genetic variation increased with popu lation size, although a small C. ownbeyi population was the most divergent. We conclude that C. ownbeyi was less abundant in Wyoming in 2015–2016 than was estimated in 1998. Causes of changes in population sizes are unknown and likely vary among populations. The positive relationship between population size and genetic diversity notwithstanding, protecting small populations can preserve unique local gene pools in this rare species.