Abstract Four major groups of Mus musculus subspecies are analysed from the genetical view point. A number of genetic traits exhibited polymorphism. Most were common among domesticus, bactrianus and castaneus subspecies, while others were musculus subspecies-specific. This suggests that the earliest differentiation was between domesticus and musculus. Mouse class I MHC was compared in these two lines. Immunological and molecular analyses of H-2K molecules indicated that these two groups of mouse have several common haplotypes of class I molecules. Phenotype frequencies of these haplotypes are considerably different in each subspecies. “Overdominance selection” in class I H-2 is one of the possible explanations for this.