Leaf trichomes may serve several biological functions including protection against herbivores, drought, and UV radiation; and their adaptive value can be expected to vary among environments. The perennial, self-incompatible herb Arabidopsis lyrata is polymorphic for trichome production, and occurs in a glabrous and a trichome-producing form. Controlled crosses indicate that the polymorphism is governed by a single gene, with trichome production being dominant. We examined the hypothesis that trichome production is subject to divergent selection (i.e., directional selection favoring different phenotypes in different populations) by comparing patterns of variation at the locus coding for glabrousness and at eight putatively neutral isozyme loci in Swedish populations of A. lyrata. The genetic diversity (H-e) and allele number at isozyme loci tended to increase with population size and decreased with latitude of origin, whereas genetic diversity at the locus coding for glabrousness did not vary with population size and increased with latitude of origin. The degree of genetic differentiation at the glabrousness locus was much higher than that at isozyme loci. Genetic identity at isozyme loci was negatively related to geographic distance, suggesting isolation by distance. In contrast, there was no significant correlation between genetic identity at the glabrousness locus and at isozyme loci. The results are consistent with the hypothesis that divergent selection contributes to population differentiation in trichome production in A. lyrata.