In this research, ISSR and SSR markers were used to analyze genetic variation of Marmareh (Prunus incana Pall.), a wild plant species from north-west regions of Iran. Totally, 12 applied ISSR primers generated 144 polymorphic bands (96.45 % polymorphism), with an average of 12 polymorphic bands per primer. Also, a total of 17 amplification alleles were detected by three SSR primers. Of these, 13 alleles were polymorphic, with an average polymorphism of 75.24 %. The similarity values based on integrating ISSR and SSR data varied from 0.07 to 0.69 between accessions, indicating high intraspecific genetic variation. Some accessions of P. incana were defined to be genetically different from the majority accessions and showed high variability, probably due to gene flow or seed propagation. The accessions collected from Sanandaj and Goshji regions were clearly differenced from others. The data generated will be useful for conservation and management of P. incana germplasm and important for Prunus breeding programs.