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Figs as an important product in recent decades due to biotic and abiotic stresses have been faced to genetically erosion. The aim of this study was to determine the genetic diversity of taxa belonged to Ficus genus using Inter-simple sequence Repeat markers (ISSR). For this purpose, 23 accessions belonging to the fig genus collected from across the Iran country and genomic DNA was extracted from leaves. Out of 18 ISSR primers pairs, six primers pairs selected and PCR process were achieved for them. A total of 83 bands were produced, of which 78 were polymorphic. Using PAUP software, through Neighbor Joining methods, 23 populations of fig were divided in four groups. Among the primers, (AG) 8 C, (TG) 8 A and (GT) 8 C were identified as the most appropriate primers for using in future studies. Based on the results obtained from the analysis of data from ISSR, 23 populations of Ficus were classified into four groups. The results of the analysis of molecular variance (AMOVA) showed that there is no difference between the taxa and the highest genetic distance between populations within species. The results of this study showed that taxa belonging to the Ficus genus in Iran are very closely related phylogentically, and the relationship between reproductive and genetic flow is high.