While there is evidence for broad-scale genetic structure in small mammals, few studies have used variable DNA-based genetic markers to examine genetic differentiation at microgeographic (tens of kilometres) scales. Yellow-pine chipmunks (Tamias amoenus) live in the heterogeneous landscape of the Rockies in southwest Alberta and are generally restricted to areas of low elevation. We used seven microsatellite loci to determine whether chipmunks show evidence of population genetic structure among three closely situated sites (< 15 km) in the Kananaskis Valley, Alberta. We found evidence for genetic structure in the form of significant differences in allele frequencies among populations and significantly nonzero values of FST for both overall and pairwise population comparisons. However, FIS values for each population were not significantly different from zero, suggesting little evidence for inbreeding within populations. Genetic differentiation probably occurs as a result of the strong effect of drift in very small (N(e) approximately 25) populations of these animals even in the face of substantial immigration rates.