It is clear that the golden age of mitochondrial DNA (mtDNA) in phylogeography has passed, but data derived from this marker have made an enormous contribution to our understanding of the process of post-glacial colonisation and other aspects of population history in many species. However, it often remains unclear how well mtDNA findings truly represent genome-wide patterns. Despite the recent advent of population genomics, it is still uncommon to have high coverage genomic studies relating to phylogeography of non-model organisms. We have been able to apply a high-throughput genotyping-by-sequencing (GBS) approach to discover and genotype 10,000+ SNP loci for 300+ bank voles (Clethrionomys glareolus) from all over Europe with the aim to determine how well the genome-wide population structure matches with mtDNA phylogeography. The knowledge of the detailed genomic phylogeography is essential to the study of adaptive differences between bank vole populations and their role in post-glacial colonisation.