Genetic analysis of the high frequency of X-Y chromosome dissociation found in primary spermatocytes of F1hybrids between Japanese wild mice (Mus musculus molossinus) and inbred laboratory mice (BALB/c) was attempted. The frequency of X-Y dissociation (X//Y) in both BALB/c and M. m. molossinus was lower than 30% (Low X//Y), while the value was more than 70% (High X//Y) in their F1 hybrids. Two types of progeny (High X//Y and Low X//Y) appeared in the backcross between BALB/c and High X//Y males, although the frequency of Low X//Y progeny decreased with increasing numbers of backcross generations (26.5% at N2, 13.2% at N3, 5.3% at N4, and 0% at N5). Low X//Y sires produced only Low X//Y mice. We hypothesize that at least one heritable factor which is responsible for the end-to-end association of the sex chromosomes (temporally symbolized as Sxa) is located on the common part of the X and Y crhomosomes. The Sxa allele of BALB/c is Sxaaand that of M. m. molossinus is Sxab. The genotype expected in High X//Y males is SxaajSxaband in Low X//Y males and their parental stocks either Sxaa/Sxaaor Sxab/Sxab. The repeated segregation of Low X//Y progeny from High X//Y sires is interpreted simply by assuming that crossing-over has occurred between the X and Y chromosomes. The gradual decrease in the recombinant type mice (Low X//Y) during sequential backcrosses suggests the presence of some autosomal factors that suppress the crossing-over of the sex chromosomes and that do not seem to function in the inter-subspecies hybrids.