Four hypervariable minisatellite loci were scored on a panel of 116 individuals of various geographical origins representing a large part of the diversity present in House Mouse subspecies. Internal structures of alleles were determined by Minisatellite Variant Repeat mapping PCR (MVR-PCR), to produce maps of intermingled patterns of variant repeats along the repeat array. To reconstruct the genealogy of these arrays of variable length, the specifically designed software MS_Align was used to estimate molecular divergences, graphically represented as neighbour-joining trees. Given the high haplotypic diversity detected (mean He=0.962), these minisatellite trees proved to be highly informative for tracing past and present genetic exchanges. Examples of identical or nearly identical alleles were found across subspecies and in geographically very distant locations while monophyly was only detected for the X-chromosome locus MMS30 in M. m. musculus, This lack of complete lineage sorting and fits well with the likely phylogeographic scenario according to which M. m. castaneus is a recent offshoot from the so-called central populations that would have occupied the speciesÕ ancestral range, while M. m. domesticus and M. m. musculus would have diverged earlier when migrating out of it. This strongly suggests that, at least for the chromosomal regions under scrutiny, wild House Mice subspecies constitute a set of interrelated gene pools still connected through long range gene flow or genetic exchanges occurring in the various contact zones existing nowadays or having existed in the past. Identifying genomic regions that do not follow this pattern will be a challenging task for pinpointing genes important for speciation.