Ziziphora tenuior, named Kakooti in Farsi, is one of the aromatic and medicinal plants of a wide distribution in Iran. In this study, RAPD molecular markers, (by utilization of 16 primers) was applied to determine the genetic diversity of 39 samples of Ziziphora tenuior from 21 geographical regions in Iran. A number of 100 polymorphic bands out of 110 amplified ones was produced and analyzed through NTsys software. Jaccard's similarity coefficient was employed to calculate similarities among the samples. Calculated similarity based on the polymorphic bands, stood in the range of 0.19 to 0.77 with a mean of 0.43. Most amplified polymorphic fragments (12) were related to the primer TIBMBA-06, while the primer TIBMBB-13 carried the lowest (3) amplified polymorphic bands. Mean number of amplified bands for primers was 6.9, while the mean number of polymorphic bands was 6.3. Cluster analysis was performed based upon similarity matrix and UPGMA method. According to cluster analysis within the similarity coefficient of 0.43, Ziziphora samples were divided into 6 groups. Based upon similarity matrix, the lowest similarity (0.19) was found for two samples from Mashhad and Eslamieh Yazd with high geographical distance whilst the highest similarity (0.77) found between two samples from Yasuj within the same geographical region. The results finally indicated high genetic diversity among the studied genotypes.