Abstract Genetic diversity between of the Novosibirsk and Tomsk chromosome races of the common shrew (Sorex araneus) was analyzed using 39 polymorphic AFLP (amplified fragments length polymorphism) markers. Exact and F-statistics tests for population differentiation demonstrated significant interracial difference in allele frequencies and significant subdivision between the races. The value of the genetic distance between the chromosome races observed in this study corresponds to that found between subspecies of mammals studied so far.