Dracocephalum kotschyi pois’ (Zarrin-Giah) is an endemic endangered medicinal plant in Iran. In this study, 30 inter-simple sequence repeat (ISSR) markers were used to detect genetic relationships among 54 wild individuals from fve endemic populations of D. kotschyi. Primers amplifed 263 bands, of which 242 (92.1%) were polymorphic. Cluster analysis, population inference, and principal coordinates analysis revealed a broad genetic variation among the populations. The highest intrapopulation diversity was observed within the Arak population. Gst and Nm mean indices of the populations were found to be 0.27 and 1.31, respectively. Analysis of molecular variance showed that the mean genetic diversities within and among the populations were 74% and 26%, respectively. The most similarity was between Isfahan and Alborz populations, whereas the least similarity was between Arak and Tehran. Based on STRUCTURE analysis, samples were divided into four groups. The fndings of this work indicate that ISSR analysis could be a suitable technique for genotyping and characterizing D. kotschyi populations. Information on diversity, found in this study, will help to conserve, domesticate and cultivate D. kotschyi for nutraceutical and pharmaceutical uses.
