One hundred and ninety-eight mice trapped along a south–north transect through the Danish hybrid zone between Mus musculus domesticus and M. m. musculus were typed for mitochondrial DNA (mtDNA), the Y chromosome and ten autosomal loci encoding diagnostic proteins. The southern (domesticus) populations display two mtDNA variants (S1 and S2) and the northern (musculus) have a third mtDNA variant (N) of domesticus origin. Across the hybrid zone defined by ten autosomal loci, there is a steep dine between the southern and northern types of mtDNA. As well as confirming an earlier finding that Danish musculus all have a domesticus mtDNA (Ferris et al. 1983a, & b), our results show that this mtDNA takeover is not the result of a persistent mitochondrial gene flow between the two subspecies. While the coincident dines for the ten autosomal loci and the abrupt dine for the Y chromosome can be explained by selection, it is less likely to be the case for the mtDNA exchanges. We discuss the possible role of sex-linked migration and genetic drift to account for the distribution of the mitochondrial variants.