RAPD markers were employed to determine the diversity among 29 genotypes and cultivars of sour and Duke cherry as well as a Mahaleb tree genotype as an outgroup. A number of 100 random primers were examined for PCR reactions on the template DNAs extracted from leaves, of which 17 primers produced polymorphic bands. These 17 selected RAPD primers produced 233 bands, among which, 214 were polymorphic. Cluster analysis of the cultivars was performed based on Dice’s similarity coefficient and UPGMA method. Genetic similarities between sour and Duke cherry samples varied from 0.40 up to 0.91. The highest similarity was detected between two sour cherry genotypes both from Hamedan orchards (collected from one place), and the lowest between a Duke cherry from Kamalshahr fruit trees collection and a sour cherry genotype from Hashtgerd orchards. Mahaleb with the lowest similarity of 0.36, stood apart from all the other genotypes individually in the cluster. At distance of 0.80 similarity in the cluster, genotypes were divided into 15 groups. Grouping of sour cherry samples at most instances was in good accordance with their origin place of growth. This reflects the close genetic background of the samples from one place due to the usual seed propagation of sour cherries in Iran. Samples of Duke cherries were separated from sour cherries and each placed in individual groups. Cophenetic coefficient between similarity matrices and the dendrogram (r= 0.92) showed the goodness of fit for dendrogram and the original similarity matrix. This survey showed RAPD markers to be useful for studies of the genetic diversity in sour and Duke cherry.