In this work the genetic variability of the common shrew populations Sorex araneus L. in Eastern Europe was studied via sequencing of the mitochondrial gene cyt b. A total of 82 sequences of the mitochondrial gene cyt b with a length of 953 basepairs were analyzed, including five chromosome races in a continuous area of the species in forest zone and two races in fragmented area in the steppe zone. Phylogeographic subdivision of the common shrew was not expressed, and there was no significant correlation between genetic and geographic distances in continuous areas. We did not acquire convincing evidence of the influence of narrow hybrid zones between chromosome races on the flow of neutral alleles. A significant p-distance (0.69 ± 0.27%) of geographically close populations of the chromosome race Neroosa indicates the formation of the karyotype of this race in the Pliocene or Pleistocene. In our work, the phylogeographic structure was determined more by species area fragmentation than by its karyotypic features.