Identification and analysis of the genetic diversity of honey bee populations is one the most important goals in the honey bees breeding. For this purpose, a total of 88 young worker honey bees from Lorestan, Esfahan, Chaharmahal and Bakhtiari, Fars, Kerman and Sistan and Baluchestan provinces were collected and subjected to molecular analysis. In the present study, total DNA was extracted from the head and thorax sections of each honey bee worker, using salting out method with minor modifications. PCR amplification of genomic DNA was performed using 10 ISSR marker primers (including: A1, A2, A3, A4, A5, A6, A7, A8, A9 and A10). The PCR products were then subjected to 1.5% Agarose gel electrophoresis. The Shannon index and Nei gene diversity index were calculated using POPGENE V. 1.31, and the molecular analysis of variance (AMOVA) was estimated by GenAlex V. 6.3. Also, the polymorphism percentage, marker index (MI), Effective multiplex ratio (EMR), and Resolving Power (RP) were calculated. The highest and lowest Shannon index were observed in A1 and A9 primers, respectively. The average Shannon index ranged from 0.248 ± 0.288 to 0.356 ± 0.286. The highest and the lowest Nei gene diversity were observed in the A1 and A9 primer. The mean Nei gene diversity in the studied populations ranged from 0.166 ± 0.201 to 0.239 ± 0.214. The highest and lowest polymorphism percentage, marker index (MI), Effective multiplex ratio (EMR), and Resolving Power (RP) were observed in A1 and A9 primers, respectively. In this study, primer A1 had the highest polymorphism. So as the best primer for the study of genetic diversity honey bee populations is recommended. Moreover, according to molecular analysis of variance (AMOVA), intra-population and inter-population genetic diversity was estimated to be 35 % and 65 %, respectively. Creating queen rearing stations and implementation of interbreeding programs should be necessary because of considerable level of genetic diversity for given honey bee populations.