The wood mouse Apodemus sylvaticus is an opportunistic rodent that is found throughout most of the European mainland. It is present on many islands around the margins of the continent and in northern Africa. The species has been the subject of previous phylogeographical studies, although these have focussed on the more southerly part of its range. A substantial number of new samples, many of them from the periphery of the species' range, contribute to an exceptional dataset comprising 981 mitochondrial cytochrome b sequences. These new data provide sufficient resolution to transform our understanding of the survival of the species through the last glaciation and its subsequent re-colonization of the continent. The deepest genetic split that we found is in agreement with previous studies and runs from the Alps to central Ukraine, although we further distinguish two separate lineages in wood mice to the north and west of this line. It is likely that this part of Europe was colonized from two refugia, putatively located in the Iberian peninsula and the Dordogne or Carpathian region. The wood mouse therefore joins the growing number of species with extant populations that appear to have survived the Last Glacial Maximum in northern refugia, rather than solely in traditionally recognized refugial locations in the southern European peninsulas. Furthermore, the existence of a northern refugium for the species was predicted in a study of mitochondrial variation in a specific parasite of the wood mouse, demonstrating the potential value of data from parasites to phylogeographical studies. Lastly, the presence of related haplotypes in widely disparate locations, often on islands or separated by substantial bodies of water, demonstrates the propensity of the wood mouse for accidental human-mediated transport.