We analyzed the genetic structure of 11 honeybee (Apis mellifera L) populations from Turkey and one from Cyprus using 9 microsatellite marker loci. Heterozygosity levels, mean number of alleles per population, number of diagnostic alleles, and pairwise F-ST values were computed for the populations studied. Heterozygosity levels were found to range between 0.54 and 0.68. We detected high levels of genetic divergence among the populations based on pairwise F-ST values; 50 of 66 pairwise F-ST values were significant. The presence of a large number of rare alleles and highly differentiated populations of honeybees are consistent with Anatolia's role as a genetic center for Middle Eastern honeybees. We suggest that certain precautions should be taken to limit introduction of foreign subspecies to preserve native genetic resources.