Maguire primrose (Primula maguirei) is a geographically restricted plant species, known only from a 19-km stretch of Logan Canyon in northern Utah (U.S.A.). We examined variation at 13 isozyme loci from 25 individuals of P. maguirei at each of eight sites. At individual loci we detected no statistically significant deviations from Hardy-Weinberg proportions within sites (subpopulations). However, some loci were almost fixed for different alleles at the upper reaches of the species’ range relative to populations approximately 10 km away. The total mean gene diversity among loci was 0.22, of which 55% was partitioned within subpopulations, 0.7% among subpopulations within populations (100 m spatial scale), 3% among populations separated by about 1 km, and 41% between an Upper Canyon group of populations and a Lower Canyon group (10-km scale). We detected no gametic disequilibria among loci within subpopulations (and populations). Two hypotheses are proposed to explain the results: (1) past genetic bottlenecks and (2) genetic divergence as a by-product of local adaptations to different habitats. Regardless of the causes of allozymic differentiation, our results suggest that plans for artificial establishment or reestablishment of P. maguirei populations should use source populations within 1 km of the establishment site. This study emphasizes the potential use of data on population genetic structure for managing and monitoring rare species.