The genetic diversity of three Iranian honey bee populations (Apis mellifera meda) was studied using morphological and microsatellite loci in south Iran. For this purpose ten morphological characters and five microsatellite loci were studied. Morphometric analysis resulted in a distinct classification of three investigated populations but showed low diversity among them. The grouping results of the diversity study by microsatellite markers were in agreement with the results of morphometry. The cluster analysis showed that the honey bees have clustered together in one group. These populations displayed low variability estimated from both the number of alleles and heterozygosity values. Genetic differentiation within the populations is low and low heterozygosity was also presented between diverse populations. These results indicate the existence of a single population structure. The results of current research confirmed us the previous findings concerning morphological and biochemical indications of uniformity in the honey bee population of the south Iran in spite of the fact that the cities which was studied by us separated from each other by a distance of 500 km.