In the light of available paleontological, genetic, and ecological data, we attempt to reconstruct the natural history of the house mouse (Mus musculus) and to justify a systematics. The house mouse is the most recent phylogenetic offshoot of the genus Mus. Its present components result from a radiation that took place most probably in the north of the Indian subcontinent about 0.5 MYA. The different colonization paths into the rest of Eurasia led to the present day subspecies: M. m. domesticus in western Europe and the Mediterranean basin, M. m. musculus from central Europe to northern China, and M. m. castaneus in southeast Asia. The central populations remain very polymorphic and are not attributable to any of these subspecies; the status of M. m. bactrianus is unclear. This radiation led to a mosaic evolution of the different parts of the genome in these subspecies. The expansion to the periphery of the Eurasian range, and more recently to the rest of the world, is related to human activity. In the case of M. m. domesticus commensalism apparently started with human sedentism in the Fertile Crescent, but its extension to the western Meditteranean basin occurred only after Neolithic times. The recent expansion has produced zones of secondary contact at the periphery of the continent. For instance, in Europe M. m. domesticus and M. m. musculus have formed a narrow hybrid zone where selection prevents the introgression of sex chromosomes. M. m. musculus and M. m. castaneus have extensively mixed in the Japanese archipelago, an intergrade in central China. The house mouse thus offers a series of replicates of the process of geographic speciation. Commensalism with humans has modified the population structure mainly through fragmentation of populations and high local densities. Possibly in relation to this way of life, M. m. domesticus has evolved many populations with various combinations of Robertsonian translocations, a choice model to study stasipatric speciation. Finally its commensalism has led to its domestication in the form of laboratory strains, which have a polyphyletic origin.