A comprehensive research of two dark-colored forest bee populations in Siberia, identified during a screening study, was conducted using morphometric and molecular genetic methods. The first population is an isolated Yenisei population located in the taiga zone in the Krasnoyarsk Territory, on which bees have not been imported for a long time (50-60 years). The second population is located in the northern areas of the Tomsk region, where beekeeping is more developed. All studied bees had a variant PQQ of the COI-COII mtDNA locus. However, some morphometric parameters of some bee colonies deviated from the Apis mellifera mellifera standard, which is probably due to the features of population formation. As a result of the analysis of the variability of 18 microsatellite loci, possible potential DNA markers specific for determining the bee subspecies and/or ecotypes of the dark-colored forest bee have been identified. An algorithm for the search and a comprehensive study of the dark-colored forest bee are proposed.