Local genetic structure has a sound theoretical basis, yet empirical demonstration in animal species has proved elusive, even in apparently ideal candidate species. Techniques based on the distribution of individual genotypes may offer a more complete picture of population structure than traditional measures focusing on isolation by distance and dispersal behavior. We used spatial autocorrelation and contiguous clustering to identify structure in a population of Richardson's ground squirrel (Spermophilus richardsonii) for which deviation from Hardy-Weinberg expectations indicated population subdivision. Nonrandom aggregates of genotypes were detected at five of six enzyme loci examined and selection at one locus. Genetic structuring was highly sex-dependent, being prominent only among females. Isolation by distance cannot account for the patterns of gene diversity observed, but Mantel matrix procedures of inter-individual distance based on demographic-behavioral characteristics and geographic distance were significantly associated. Social and breeding systems of S. richardsonii lead to significant local substructure. While philopatry alone may not account for fine-scale genetic structure in small mammals with sex- biased dispersal, nonrandom aggregates will be detected if appropriate social models and rigorous sampling criteria are adopted. Identification of such localized structure remains fundamental to understanding evolutionary models of population genetic structure and sociality.