Variability of the nucleotide sequences of the second intron of the b1-chain of hemoglobin (Hbb-b1) and complete control region of mitochondrial DNA (D-loop) was studied in aboriginal and commensal populations of M. m. wagneri from Central Asia and M. m. gansuensis from South Siberia. A difference in frequency of the hemoglobin Hbb(w1) type for natural and urban populations of mice was shown. All mice from natural habitats of studied areas kept musculus-type of mtDNA. Apparently, the substitution of taxonpecific mitochondrial haplotypes of wagneri and gansuensis might occur due to absorbing hybridization with nominate subspecies musculus, what is consistent with the results on nuclear DNA (Hbb-b1 gene) of this work. Two differentiated haplo groups among aboriginal subspecies wagneri were discovered first time (d = 0.01), one of which included house mice from Turkmenistan. This may indicate on mtDNA introgression from commensal forms of Turkmenistan into natural populations of Kazakhstan mice. The castaneus-type of mtDNA was detected in two individuals from the natural habitat of Kazakhstan and Turkmenistan, it had not been met in Central Asia before. It is suggested that the gene flow of nuclear and mitochondrial genomes in microevolution processes in M. musculus is directed from the commensal forms towards wild populations.