SSRs are one of the most suitable DNA-markers for assessment of genetic diversity of plant genetic resources. Microsatellites were used for development of saturated genetic maps of apple (Malus × domestica Borkh.) as well as for wide range of genetic diversity studies. Our study was aimed on the investigation of the genetic relationship within subcollection of modern Russian apple cultivars. Polymorphism of 12 microsatellite loci was estimated for 31 apple cultivars from the SKZNIISiV collection of genetic resources. These cultivars have been bred in North Caucasian Regional Research Institute of Horticulture and Viticulture (SKZNIISiV) and All-Russian Research Institute of Fruit Crop Breeding (VNIISPK). SSR-markers CH01f03b, CH01h01, CH01h10, CH02c06, CH02d08, CH04e05, CH05f06, CH01f02, CH02c11, Hi02c07, CH02c09 and CH03d07, which are recommended by Fruitbreedomics, the European consortium, were used in the study. According to the data of SSR-analysis from 5 to 10 alleles per locus were detected, with an average value of 7.75 alleles per locus. A total of 93 alleles were detected for all 12 loci. All apple cultivars showed individual, distinct SSR-profiles. Comparison with the data on the genetic diversity of the world apple tree gene pool suggests that the SSR-loci polymorphism in studied set of the apple cultivars is relatively high. Expected (He) and observed (Ho) heterozygosity varied within the ranges of 0.548-0.897 and 0.602-0.827 for Ho and He, respectively. The average values of these indexes are Ho = 0.786 and He = 0.755. PIC value ranged from 0.571 to 0.806, and 9 loci showed PIC value higher than 0.712. Results of UPGMA-analysis are consistent with the level of genetic heterogeneity of the studied cultivar set.