Genetic structure of bank vole populations in linear river bank habitat in southeast Norway was determined from analyses of DNA sequences for the mitochondrial D-loop. Animals were sampled at sites separated by 1 km, along two forested river banks separated by ≈ 100 m of open water. Twenty-six distinct haplotypes were found among 120 voles. The voles showed significant deviation from panmixis on both sides of the river. Animals from the same site or from sites 1 km apart were more likely to share haplotypes than animals 2 km apart or more. Common haplotypes were widespread on both river banks, and had a wider distribution than relatively rare haplotypes. Some rare haplotypes were found on both banks, but most were restricted to a single bank. The results suggest that short-term gene flow may be restricted for female bank voles in linear habitats. Female territorial behaviour may vary with habitat geometry. In the linear habitat described here, females defend only two territorial borders and may effectively limit female dispersal. Results were compared to a previous study of bank voles from this region in a two-dimensional habitat. Gene flow in the linear habitat was much more restricted than gene flow in the two-dimensional habitat. Probable mechanisms underlying this difference are discussed.