Genetic variation within and among populations is the basis for survival of the populations both in short and long term. Thus, studying the plant genetic diversity is essential for any breeding program. Rosa damascena Mill., is an important species as a source of rose oil, and is one of the oldest rose species grown in Iran. The main rose oil producers in the world are Turkey, Bulgaria and Iran. They are obtaining the rose oil almost exclusively from the certain clones of R. damascena. This study was conducted to detect the genetic variability and relationships across 6 Damask rose populations from Kashan region (Barzuk, Niasar, Azeran, Aheste, Kheirabad and Kolpe) and one from Hamedan province (Bahar). Nine plants (on average) per population (in total 54 plants) were used for genotyping by 11 ISSR (Inter simple sequence repeat) and 9 RAPD (random amplified polymorphic DNA) markers. ISSR markers produced 91 bands, of which 41 were polymorphic (67%). Primer ISSR7 and ISSR24 detected the highest percentage of polymorphism, while for primer ISSR19 the lowest one was observed. RAPD markers produced 81 bands, of which 54 were polymorphic (66%). Primers R10 and R7 detected the highest percentage of polymorphism, while primer R4 was the lowest. UPGMA cluster analysis based on Jaccard similarity coefficient by ISSR markers revealed nine groups in the dendrogram and genetic similarity ranged between 0.61 to 0.98. By RAPD markers, nine clusters were also obtained and genetic similarity ranged between 0.57 to 0.97. In both marker types, differences between the plants within the populations were very low, however considerable genetic diversities detected between the evaluated populations. Aheste and Hamadan populations had the greatest difference and genetic distance. Hamadan samples had the closest relationship with individuals of Kolpe and Kheirabad. RAPD and ISSR markers provided useful tools for evaluating genetic diversity and genetic relationships of R. damascena. The kno
