Current phylogenetic analyses of relatively long sequences of mitochondrial DNA (4,225 bp) in the Japanese house mouse Mus musculus provided the first evidence that both southern Asian subspecies of Mus musculus castaneus (CAS) and northern Asian subspecies of M. m. musculus (MUS) arrived in Japan through rapid population expansion events, from Southern China ~4,000 years ago and the Korean Peninsula ~2,000 years ago, respectively. Nuclear DNA haplotype structure analyses targeted a chromosome region with two different tract sizes, 1 Mb and 5 Mb, consisting of nine and six tandemly arranged markers, respectively, yielding a possible average fragment length of 170 kb of CAS haplotypes in the MUS background genome in northern Japan, providing a rough estimate of its elapsed time of 815 generations under an assumption of continued backcrossing. Less frequent and shortened CAS-like haplotypes specific to Japan were detected, suggestive of ancient introduction prior to the appearance of the South Chinese CAS in Japan. Our analyses also showed sporadic appearance of long fragments (2-5 Mb) from the west European subspecies M. m. domesticus, indicating contemporary stowaway introduction. Overall, multiple overseas introductions, and the time-lagged inter-subspecies genetic admixture, likely resulted in the heterogeneous state of Japanese wild mice.