Aim It has been proposed that the root vole subspecies, Microtus oeconomus finmarchicus, survived the last glacial period on islands on the north-west coast of Norway. The Norwegian island of Andoya may have constituted the only site with permanent ice-free conditions. Geological surveys and fossil finds from Andoya demonstrate that survival throughout the last glacial maximum was probably possible for some plants and animals. In this study we aim to infer the recent evolutionary history of Norwegian root vole populations and to evaluate the glacial survival hypothesis. Methods DNA sequence variation in the mitochondrial cytochrome b gene was studied in 46 root voles from 19 localities. Location Northern Fennoscandia and north-west Russia with a focus on islands on the north-west coast of Norway. Results The phylogeographical analyses revealed two North European phylogroups labelled 'Andoya' and 'Fennoscandia'. The Andoya phylogroup contained root voles from the Norwegian islands of Andoya, Ringvassoya and Reinoya and two localities in north-west Russia. The Fennoscandian phylogroup encompassed root voles from the three Norwegian islands of Kvaloya, Hakoya and Arnoya and the remaining specimens from Norway, northern Sweden and Finland. Nucleotide diversity within the Andoya and Fennoscandian phylogroups was similar, ranging from 0.5% to 0.7%. Main conclusions Both our genetic data and previously published morphological data are consistent with in situ glacial survival of root voles on Andoya during the last glacial maximum. However, the level of genetic diversity observed in the extant island populations, the past periods of severe climatic conditions on Andoya and the ecology of the root vole are somewhat difficult to reconcile with this model. A biogeographical scenario involving late glacial recolonization along the northern coasts of Russia and Norway therefore represents a viable alternative. Our results demonstrate that complex recolonization and extinction histories can generate intricate phylogeographical patterns and relatively high levels of genetic variation in northern populations.