Samples from seven honey bee populations; five Apis mellifera meda from Iran and two from Turkey, one belonging to A. m. meda and one to A. m. caucasica, were investigated using morphometric, mtDNA, and microsatellite analyses. Morphometric analysis revealed three distinct clusters. The first included all Iranian populations, whilst the second and third contained the meda and caucasica bees from Turkey. No variation was observed in the DraI restriction of COI-COII intergenic region in mitochondrial DNA, yielding a single C lineage mitotype. The analysis of microsatellite loci, A7, A24, A28, A43 and A113 revealed, a considerable level of genetic diversity, with average expected heterozygosity ranging from 0.596 +/- 0.188 to 0.695 +/- 0.174 and average number of alleles per locus from 4.4 to 8.0 among Iranian honey bee populations.