The purpose of our study was to estimate genetic diversity of Prunus avium in natural populations. Genetic studies were carried out in 27 wild cherry populations sampled from several Polish tree stands. Chloroplast DNA variation was assessed and two haplotypes were identified. Theirs distribution divided populations into two groups. Haplotype H1 was present in 11 of 27 populations and H2 in 16 populations. The PCR−
−SSR technique was used to detect nuclear DNA diversity. Three highly polymorphic SSR (microsatellite) primer pairs were used to describe the genetic variation. Heterozygosity values ranged from 0.500 to 0.633, while gene diversity (PIC) from 0.75 to 0.79. This study demonstrated that SSR fingerprinting with cpDNA diversity, can be used for preliminary characterization of Prunus avium populations