For the first time, we attempt to study the phylogeny of the Crocidura suaveolens s. l. species complex using multilocus analysis. Sequencing data for 16 nuclear genes indicate the existence of several distinct forms within the species complex, and its structure does not in general contradict mitochondrial phylogeny. Siberian shrew is characterized by some specificity of the nuclear genome, but the degree of its genetic differentiation does not correspond to species-level. We clarified the relationships of Crocidura aff. suaveolens from South Gansu and Sichuan with other forms of the species complex. The shrews from Buryatia and Khentii also belong to this form, but their mtDNA had apparently introgressed in the past from C. shantungensis. In the recent time, hybridization of C. suaveolens s.str. with C. aff. suaveolens and C. güeldenstaedtii, had also occurred. Taking into account multiple introgression events in the history of C. suaveolens s.l., for the analysis of the phylogenetic relations between its forms a significant increase in the set of loci is required.