Iranian honey bee ( Apis mellifera meda ) is one of the 24 honey bee suecies in the world which could be found not only in Iran, but also in Northern Iraq, South East Turkey and even Northern Syria. In terms of morphological characterization, this suecies is seemingly similar to A. m. liguistica , from Italy. Taking biological properties into consideration, this suecies has tendency to high swarming and propolis gathering strength, great overwintering capability and high invasive behavior, all of which distinguishe this race from others. As for variability maintenance among species and genetic reserve identification, and regarding the fact that the first step to fulfill purposeful breeding is to determine genetic diversity in the populations, the aim of this research was to assess genetic diversity in Iranian honey bee population all over the country, using microsatellite molecular markers. Microsatellites as DNA markers have been widely used in many studies to determine genetic variations honey bee population in the world, widely. The samples were collected from 18 populations belonging to eight provinces including Khorasan Razavi, Semnan, Mazandaran, Alborz, Zanjan, Hamedan, West Azarbayejan and Isfahan. After DNA extraction using a CTAB protocol and optimization of PCR amplification, all the loci were well amplified and PCR products were visulized on 12% non-denaturing polyacrylamide gel. In this study, genetic diversity was assessed using ten pairs of SSR primers that generated between 11 to 26 alleles with average of 21.9 alleles per primer and revealed high (0.991) expected heterozygosity. Based on the obtaind SSR dendrogram using Power Marker V.3.25 software, Iranian honey bee population divided into four clusters. Clustering of Iranian honey bee populations using SSR markers was in concordance to geographical distribution. Using analysis of molecular variance (AMOVA), it was shown that significantly differentiation exists among honeybee populations (p 0.001). Intra-population and inter-population genetic diversity were assessed to be 90.57% and 9.43%, respectively. The results indicated high genetic diversity among Iranian honey bee populations and intra-population genetic diversity was higher than inter-population genetic diversity in studied populations. . Keywords: Iranian honey bee, Genetic diversity, Microsatellite, Analysis of molecular variance