An assessment of the genetic diversity of the COI-COII mtDNA locus in honeybee populations from the Tomsk region was conducted. Three variants of the COI-COII mtDNA locus were registered: PQQ, PQQQ (typical for Middle Russian race), and Q (typical for southern breeds). It was established that 64% of bee colonies of the maternal line originate from the Middle Russian honeybee race, 28% of bee colonies originate from southern species, and 8% are mixed bee colonies. The southern parts of the region show a higher genetic diversity of honey bees as compared to northern regions, which are dominated by bee colonies (96%) and apiaries (73%) that are homogeneous for the genetic variant of locus COI-COII. The Tomsk region has no large areas with bee colonies maternally originating from the Middle Russian breed; only a few apiaries (both in the northern and southern areas) were revealed in which all bees originated from the Middle Russian breed.