Previous reports of mitochondrial DNA variation in Japanese mice have revealed the occurrence of two components, a M. m. musculus mtDNA type in central Japan and a M. m. castaneus one at both northern and southern ends. In the present study, we explore the genetic composition of nuclear genes from Japanese wild mice. Protein electrophoresis at 16 polymorphic loci was used to characterise mice from 20 localities and to compare them with samples from the surrounding countries. The results revealed a predominant M. m. musculus nuclear gene component on the main Japanese Islands. A M. m. castaneus contribution was detectable in south Kyushu, but, interestingly, not evident in Northern Honshu were the castaneus mtDNA predominates. On the other hand, the mouse populations from Ogasawara (Chichi Islands) showed a threefold origin with a strong M. m. domesticus component, probably resulting from a very recent admixture. This clearcut example of reticulate evolution, which does not give rise to an homogeneous gene distribution, is however very different from the situation observed in the European hybrid zone. This raises questions concerning the mechanisms that either impede or favour gene admixture when differentiated gene pools are brought together.