In this study the results of analysis of the genetic structure of bees samples from six northern districts of the Republic of Bashkortostan (Baltachevsky, Birsky, Blagoveshchensky, Buraevsky, Tatyshlinsky and Yanaulsky) were presented. First, using the analysis of the intergenic locus COI-COII, belonging to the evolutionary lineages M (A. m. mellifera) or C (A. m. carnica, A. m. caucasica, A. m. ligustica) was established. Then, in bee colonies A. m. mellifera, the level of introgression of the gene pool of evolutionary lineage C was established based on the polymorphism of 9 microsatellite loci of nuclear DNA. As a result, the lowest level of hybridization was detected in samples from Yanaulsky, Tatyshlinsky, Buraevsky and Baltachevsky districts. The highest level of hybridization was detected in colonies from Birsky and Blagoveshchensky districts. In addition, in these two areas, a large number of colonies from the evolutionary lineage C were identified.