Dracocephalum thymiflorumL. is a medicinal plant that grows in limited areas in Iran and forms few local populations. We have no information on its genetic diversity and population genetic structure in the country. Therefore, the present population genetic study was performed to provide data on population genetic structure, potential gene pools and gene flow in Dracocephalum thymiflorumin Iran. The information obtained can be used in conservation of this medicinal plant species. We studied 55 randomly selected plants from 5 geographical populations by ISSR molecular markers. The studied populations contained high within-population genetic variability and also revealed strong genetic differentiation by AMOVA test (P = 0.01). Structureanalysis and K-Means clustering revealed population genetic fragmentation that was mainly due to genetic difference between population 2 and the otherstudied populations. The population assignment test revealed the occurrence of limited gene flow among these populations. The information obtained can me used in programming the conservation of this important medicinal plant in Iran
