The aim of this study is to determine genetic diversity within Prunus angustifolia and also to investigate its phylogenetic relationship with Prunus avium, Prunus cerasus, Prunus laurocerasu s and Prunus mahaleb . Totally 50 SSRs markers were used to elucidate the genetic variation among 32 P. angustifolia var. angustifolia genotypes selected in Northeastern Turkey. The cross-species transportability of used 50 SSRs was 80% indicating a high degree of homology between P. angustifolia and the other Prunus species. The genetic distance between P. angustifolia var. angustifolia genotypes belonging to a particular geographic site was lower than that between genotypes of different geographic origins. Cluster analysis in general differentiated P. angustifolia var. angustifolia genotypes according to their geographic sites and separated them from the other Prunus species. P. angustifolia was found closer to P. mahaleb and P. cerasus . The analysis of molecular variance (AMOVA) revealed that genetic variation among individuals within populations was much higher than among Prunus groups and among P. angustifolia var. angustifolia populations of different geographic sites.