Turkey is an important producer of cornelian cherries (Cornus mas L.), especially in northern Anatolia. Seed propagation and long-term human selection has given rise to a great diversity of trees. Twenty-six cornelian cherry genotypes (CC1–CC26) from the Coruh Valley in northern Anatolia were evaluated for genetic relationships by using Randomly Amplified Polymorphic DNA (RAPD) markers, based on 56 decamer random primers, seven of which showed reliable polymorphisms. These seven primers generated 80 markers, with 77 (96.25%) displaying polymorphisms. Cluster analysis of the cornelian cherry genotypes was performed based on data from polymorphic RAPD bands, by using Jaccard's similarity coefficient and the Unweighted pair-group method with arithmetic average (UPGMA) clustering method. A similarity matrix showed that the highest genetic similarity (0.913) was between CC15 and CC16 and the least (0.129) was between CC4 and CC16. The cophenetic correlation coefficient between the similarity matrix and the cophenetic matrix of the dendrogram was relatively high (r = 0.87), supporting the validity of the dendrogram. Based on these results, RAPD analysis can be used for the characterization and grouping of cornelian cherry genotypes. Genetically divergent genotypes identified in this study may be useful for future breeding programs. This is the first study demonstrating that RAPD analyses can be used to differentiate and classify cornelian cherry genotypes.