The study of the genetic diversity of Ukrainian sweet cherry cultivars using DNA markers is important for targeted breeding research, control of cultivar identity and genetic stability of clones, management of collections of genetic resources and protection of breeders' rights. The genetic fingerprinting of Ukrainian sweet cherry cultivars and accessions (total of 110 genotypes) was conducted using several types of molecular markers (MM): IRAP, REMAP, ISSR, SSR. The discriminatory capacity of the markers was evaluated. Also, the most suitable MM for routine use and the minimal sets of microsatellite loci required for genotyping were determined. We created genetic profiles of the cultivars and complemented the cultivars passports with these profiles, as well as evaluated the genetic relatedness of the genotypes. The analysis of the genetic structure of 94 cultivars reveals the existence of ten gene pools, four of which were previously unknown. Genetic pools 4 and 10 include cultivars, which were probably obtained using some landraces and other forms of local origin. Genetic pools 6 and 9 are predominantly formed by F1-F3 progeny of Drogans Yellow and Valerii Chkalov. Allelic variants of the PavCNR12 and the S-locus genes that control economically important traits were identified. A new convenient method for the identification of allelic variants of the PavCNR12 gene using codominant CAPS-markers is proposed. Applying this method, the allelic status of PavCNR12 was elucidated for 70 sweet cherry cultivars of Ukrainian and foreign breeding. A significant prevalence of the desirable allele PavCNR12-1 over alleles PavCNR12-2 and -3 was found among the studied cultivars. S-genotypes were determined for 70 local sweet cherry cultivars, promising breeding clones, 10 wild accessions of Ukrainian origin and 14 foreign cultivars. In total, 14 different S-alleles were detected. The most common S-alleles were S1 (12.5%), S3 (14.9%), S4 (8.3%), S5 (18.5%), S6 (13.1%) and S9 (21.4%). The relative occurrence of the identified S-alleles confirms that the studied cultivars belong to the European group of origin. Characteristic is the domination of the S5 and S9 alleles, which distinguishes the cultivars of Ukrainian origin from other European ones. All analyzed cultivars were classified into 17 known cross-incompatibility groups (CIG). The largest groups are CIGs XXXVII (S5S9), VII (S3S5), X (S6S9) and XVIII (S1S9), which include 12, seven, six and six cultivars, respectively. Most rare are cultivars, which belong to the CIGs II (S1S3), VI (S3S6), XV (S5S6), XXVII (S4S12), XLIII (S2S9), XXX (S6S7) and XVII (S4S6). The cultivar 'Yedyna' was an exception since it carries the alleles S6 and S17 and was placed in the group O as a universal pollinator.
