Restriction fragment length polymorphisms (RFLPs) of maternally inherited mitochondrial DNA have revealed that genetic exchanges can occur between populations, subspecies or even species. From the point of view of population genetics the mammalian Y chromosome represents a genomic analogue of the mitochondrion; it is inherited only paternally and remains perpetually monosomic, showing little meiotic recombination with other chromosomes. Using a Y-specific genomic DNA probe obtained from a flow-sorted mouse Y-chromosome library, we have examined the RFLPs in 10 newly established mouse lines of the European semispecies Mus musculus domesticus and Mus musculus musculus, and identified two variant forms of the Y chromosome, each of which is characteristic of one of the semispecies. As reported here, probing the DNA from nine established inbred laboratory strains reveals that the strain SJL carries a M.m. domesticus type Y whereas, surprisingly, the Y chromosomes of the other eight strains are of M.m. musculus origin. Hence, these strains cannot be regarded as archetypes of M.m. domesticus as suggested by protein polymorphisms and mitochrondrial DNA sequence data, but rather as genetic hybrids between the two semispecies.