Twenty-two G. glabra populations were used to study the genetic diversity of ISSR molecular markers. 12 primers were used to amplification of genomic DNA fragments of G. glabra populations. High genetic diversity based on ISSR markers was observed among individuals. A total of 130 bands were formed and 105 bands were polymorphic. The mean polymorphism percentage among studied populations was 80.47. The highest polymorphic percentages were assigned to IS23, IS21, IS9, IS13 and IS15 primers. The mean of PIC and MI were 0.347 and 2.47, respectively. The Shannon index (I) varied between 0.207-0.393 and the Nei genetic variation index (h) from 0.140 to 0.026. Darab and Solataniyeh populations showed the lowest and highest genetic diversity, respectively. The percentage of polymorphic loci was varied between 35.224 to 65.71%. The observe allele number and effective alleles number was 1.46 and 1.34, respectively. Based on the genetic distance Nei, populations Bardsir and Baft had the highest genetic similarity (0.888) and populations Bardsir and Solataniyeh had the least genetic similarity (0.132). The studied populations were grouped into three main groups by cluster analysis using UPGAM and Jaccard's similarity coefficient. The results showed that the ISSR marker is a reliable marker system for revealing a high level of polymorphism and can be used to study genetic diversity and further examinations as a subset of breeding programs in G. glabra.