Supported by Russian Science Foundation, project ¹ 14-36-00039 Received September 26, 2016 A b s t r a c t With the publication of the complete sequence of a cattle genome, it became possible to trace the history of breed origins and to evaluate genetic relationships between modern breeds, based on the results of genome-wide SNP screening. <...> Whilst numerous studies have been undertaken to characterize the commercial breeds and some local cattle breeds of Europe, North America, Asia and Africa at whole-genome level, little is known about genetic differences, relationships and population genetic structure of the Russian native cattle breeds. <...> The aim of our work was to study the genetic diversity and population structure of five locally-developed Russian cattle breeds, based on genome-wide single nucleotide polymorphisms (SNPs) generated using Illumina Bovine SNP50 BeadChips (Illumina, San Diego, CA, USA). <...> In total, 116 samples (sperm or tissue) collected from five breeds were analyzed, including Bestuzhev (BEST, n = 27), Kholmogor (KHLM, n = 25), Kostromsky (KSTR, n = 20), Red Gorbatov (RGBT, n = 23) and Yaroslavl breeds (YRSL, n = 21). <...> Samples of Holstein cattle (HLST, n = 29) were used for comparison. <...> Quality filtering of genetic markers was performed in PLINK v 1.07. <...> The final set of markers passed through the quality control and selected for further analysis included 35874 SNPs. <...> Average heterozygosity within breeds ranged from 0.378 in BEST to 0.390 in KHLM and was higher comparing to HLST (0.377). <...> The multidimensional scaling (MDS) showed the presence of non-overlapping breed specific clusters, whereas the first principal component (PC1) accounted for 5.46 % and the second principal component (PC2) was responsible for 5.05 % of the genotypic variance. <...> Phylogenetic analysis based on parsimony method grouped individuals into six clusters according to their breeds. <...> The STRUCTURE analyses supported the assumption that the ancestry of the locally developed Russian cattle breeds is distinct from Holsteins and Holstein-related breeds. <...> Analysis of molecular variance (AMOVA) showed highly significant results for genetic differentiation (p < 0.001) in studied breeds. <...> The emerging structure of the phylogenetic tree constructed on the Nei genetic distances, is in full concordance <...>