Whole-genome analysis opens the new possibilities to characterize the genetic structure of population and to evaluate the biodiversity in agriculture animal species. The aim of our study was to investigate genetic diversity for local cattle breeds from Central and Northeast European parts of Russia and Siberia in comparison with dairy cattle breeds using the whole-genome SNP data. The total of 57 animals from 5 different breeds were genotyped by 50K Illumina BeadChip including Yaroslavlskaya (n = 5), Kholmogorskya (n = 8) and Yakutian cattle (n = 7) as well as widespread Russian Black-and-White (n = 6) and Holstein (n = 30). Quality control and analysis was performed using PLINK (1.07), while 1119 loci with > 10% of missing data were excluded, 7069 SNPs failed test frequency minor alleles (MAF < 0.01) and one bull was removed with missingness rate > 10%. 46596 SNPs were left for further analysis. A total of 2660 heterozygous haploid genotypes with the genotyping rate 0.992 were revealed. All local breeds characterized by deficient of SNP heterozygotes. Values of index fixation (F) were positive and ranged from 0.57% in the Russian Black-and-White breed to 17.56% in the Yakutian cattle. The genomic inbreeding coefficient was 3.99%, 4.17% and 10.39% for Holstein, Kholmogorskya and Yaroslavlskya breeds, respectively. Runs of homozygosity (ROH) in all investigated animals were 7.64Mb in average wherein minimal ROH was observed for Kholmogorskya, Yakutian and Yaroslavlskya breeds (6,65Mb, 7.25Mb and 7.39Mb,respectively) while for Holsteins and Russian Black-and-Whites were characterized by the maximum value of ROH in 7.97–8.00Mb. Linkage disequilibrium in the data set was r² = 0.40. The principal component analysis based on pairwise identity-by-state distances confirmed that there was the clear clusterisation among animals of Russian local cattle breeds and the group of Black-and-White and Holstein breeds. The greatest genetic difference was shown between Yakutian, Yaroslavlskya, and Kholmogorskya breeds as well as between Yakutian and the populations, which were assigned to branch of Holstein cattle. Supported by the Federal Agency for Scientific Organizations, Theme number 19.3 and Russian Scientific Foundation, project number 14–36–00039.