The complex species Mus musculus is widespread in Eurasia and consists of four parapatric genetical entities (subspecies) that have recently radiated. Two of them (M. m. domesticus and M. m. musculus) are known to interact through a narrow zone of hybridisation across which autosomal and mitochondrial exchanges are very limited and Y chromosome exchange is absent. We extend here the study of this group by the genetical analysis of 22 Asian strains of various origins (China, Korea, Japan, Taiwan, Philippines and Indonesia). A survey of protein variation at ten polymorphic loci confirmed that these animals belong to either the subspecies M. m. musculus (northern type in Asia, ranging westwards to Eastern Europe) or to M. m. castaneus (southern Asian type) and revealed a certain degree of intergradation between the two taxa. Y chromosome variations were assessed in these strains using a Y specific DNA probe representing part of a small multigene family and also in four M. m. domesticus (the Western European house mouse) strains of various origins and one M. m. bactrianus (from Pakistan). Musculus and castaneus were identically monomorphic for one type of organisation of this Y repeated family, while domesticus and bactrianus were very similar to each other, showing slightly different types of organisation. Introgression of a bactrianus Y chromosome into the territory of castaneus was found in Indonesia. The present distribution of the Y types among the four subspecies is not phylogenetically concordant with the known distributions of autosomal and mitochondrial variants.(ABSTRACT TRUNCATED AT 250 WORDS)