The sex-related spatial genetic structure of a free-living population of the common vole (Microtus arvalis) was assessed using sequence and haplotype frequency data of the complete mitochondrial cytb gene in three seasons. Six haplotypes were resolved, three of them (A, B and C) were shared among seasons and sexes. The remaining three singletons did not match any of the local females. Pairwise tests did not show significant differences in haplotype frequencies between seasons. However, we observed such differences between the sexes. The aggregation index calculated for haplotype B showed a clumped female spatial distribution and revealed two clusters of the matrilineal lineage in the population. The female effective population size (N_ef) estimated from shifts of haplotype frequencies between seasonal samples was quite small and the N_ef/N_f ratio ranged from 0.18 to 0.35. We suggest that both factors, low N_ef and female philopatry may be responsible for considerable inter-population differentiation previously reported in this abundant vole species.