The genetic diversity of the honey bee (Apis mellifera ) remains undescribed in some parts of its natural
distribution range, concretely in those subspecies inhabiting central and southeastern Europe: the globally distributed A. m. ligustica and A. m. carnica, and A. m. cecropia and A. m. macedonica. In this study, we add further
information about their genetic variation, differentiation, and admixture using maternal and codominant
(microsatellites) molecular markers. The phylogeographic analysis demonstrated the distinct distribution of mitochondrial haplotypes across the sampled geographic range. Cluster analysis detected two main groups of colonies while further discriminant analysis of the principal components supported the existence of ecotypes within A. m carnica and A. m. macedonica , and admixture of them. The extent of introgression and the presence of foreign
haplotypes in some of these populations suggested that introductions of non-native subspecies represent a serious
threat to the genetic integrity of native honey bee populations due to the creation of hybrid populations. Keywords: Apis mellifera; Central and southeast Europe; conservation; ecotypes; genetic diversity
