The western house mouse Mus musculus domesticus is a human commensal, and as such, its phylogeography relates to historical human settlement patterns and movements. We investigate the phylogeography of house mice in northern France and the British Isles (particularly Ireland and the Scottish islands) using microsatellite data and mitochondrial (mt) control region sequences from modern and museum material, placing these in a Europe-wide context. The majority of mtDNA sequences from northern France belong to a clade widespread across the British mainland and Germany, supporting an earlier suggestion that this clade distribution represents colonization by house mice in the Iron Age. The presence of the clade in south-western Ireland indicates possible Iron Age colonization there as well. However, the majority of the Irish sequences belong to a clade elsewhere associated with Norwegian Viking activity, and likely represent the main wave of house mouse colonization of Ireland, arriving from the Scottish islands during the Viking period and linked to urbanization. The St Kilda sequences (from 100-year-old museum samples of the extinct form 'Mus muralis' of Barrett-Hamilton) and sequences from South Uist and Lewis also belong to this clade. The clustering of populations shown by the microsatellite data is distinctly different from the mtDNA phylogeny, with populations grouping by geographic proximity, possibly reflecting the genetic effects of secondary colonization. When the mtDNA sequence data are placed in a Europe-wide context, it is clear that the distributions of the two prevalent clades from the vicinity of the British Isles are essentially limited to north-western Europe. These two clades show no evidence of expansion through central Europe, and may therefore reflect maritime colonization.