Practice of commercial honey bee breeding and selection for desired traits, intensification of queen importation and migration of once stationary apiaries significantly influences distribution and genetic diversity of local subspecies, populations and ecotypes. Bee colonies worldwide are facing serious declines resulting in colonies loss and reduction of genetic diversity. Thus, reassessing the genetic status of native honey bee populations becomes imperative. The latest reports, which include samples from nine years ago, suggest the presence of both Apis mellifera carnica in north and A. m. macedonica in the south of Serbia and significant hybridization between two subspecies.

To assess genetic diversity of contemporary managed honey bee colonies we used 14 microsatellite loci and analyzed 227 worker bees from 46 apiaries in 8 localities from northern and southern Serbia. RFLP analysis on the COI gene segment of mtDNA was used to distinguish A. m. carnica from A. m. macedonica. Mean number of alleles ranged from 5.14 to 9.00, observed heterozygosity from 0.43 to 0.56 and STRUCTURE analysis showed existence of three distinct genetic clusters. DAPC analysis showed huge overlapping of individuals from different parts of Serbia with weak clustering according to geographical origin of three groups. RFLP analysis showed the presence of A. m. carnica subspecies only.

Absence of A. m. macedonica subspecies from its historic range of distribution in southern Serbia as well as lack of distinctive geographical clusters suggest that selective breeding, queen import and migratory beekeeping practices strongly influenced genetic structure and diversity of honey bees leading to the genetic uniformisation and absence of locally adapted populations.