The bank vole (Clethrionomys glareolus) represents an important model species in studies of adaptive phylogeography aimed at elucidating the role of selection in postglacial recolonisation. Functional variation in haemoglobin (Hb) distinguishing two bank vole populations that successively colonized Great Britain from different glacial refugia presumably helped facilitate the population replacement. The two Hb variants are distinguished by a single amino acid substitution of serine by cysteine in the beta globin chain. The presence of extra cysteine in haemoglobin carried by the second colonising population demonstrably increases the antioxidant capacity of the red blood cells and it thus may have had a role in determining the adaptive advantage over the first colonists. Here, we found that both Hb variants are widely dispersed in continental Europe, showing a clear geographical pattern with each variant exhibiting association with a different phylogeographic lineage, as defined by mtDNA. This supports the functional differentiation of Hb between different refugial populations of the bank vole. The results from spatial analysis show that environmental conditions have a significant predictive value on Hb allele frequencies, which supports the hypothesis of the Hb divergence (and hence selection) being important in determining which glacial refugia were ultimately successful in populating the current bank vole distribution.