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Analysis of levels and patterns of genetic variation in a rare species is important for determining whether genetic factors associated with small population size, such as genetic drift or inbreeding, may be negatively affecting a species. In this study, we compared estimates of genetic diversity and patterns of population genetic structure in a rare cliff endemic, Erigeron lemmonii, to those of a widespread congener, E. arisolius. Our goals were to assess whether rarity and small population size have negatively affected levels of genetic diversity in E. lemmonii and to identify genetic threats that may limit the ability of E. lemmonii to persist. Levels of observed and expected heterozygosity and allelic richness in E. lemmonii were approximately 60 % of those found in E. arisolius. After correcting for null alleles, inbreeding coefficients in both species of Erigeron were very small, suggesting that both species are highly …