Diversity of ecological conditions in Anatolia enables many species to adapt to different environments. Thus Turkey is inhabited by various strains of A.m. mellifera Linnaeus, 1978; A.m. mellifera carnica, A.m. mellifera anatoliaca, A.m. mellifera caucasica, A.m. mellifera syriaca, and A.m. mellifera meda. Analysis of mtDNA variants is a widely used tool to determine the phylogenetic relationships at the species and subspecies levels. In this study sequencing results of tRNA(leu)-00X2 and ND5 gene segments of mtDNA were presented in comparison with some previously published mitochondrial haplotypes. According to the UPGMA dendogram and estimates of evolutionary distances, divergence among the subspecies and ecotypes were not verified strongly. Reproductive isolation barriers could be uneffective and lead to the exchange of the genetic materials between the populations. Intensive care should be taken while managing the colonies of different subspecies in bee yards. Degradation of biodiversity of honey bee subspecies through hybridization was also reported at wider geographic areas rather than small breeding units in some studies. Broad ranges of isolated colonies of subspecies should be established with proper selection studies to reduce the hazards of migratory beekeeping activities. Succesful management practices are needed through better beekeeping technologies and beekeeper training programmes to prevent the homogenization of the genetic structure of different subspecies and to conserve honey bee diversity.