Creating panels for parentage assignment based on the most informative SNPs (minor allele frequency, MAF≥0.3) is an important problem of the modern sheep breeding. International Society of Animal Genetics (ISAG) recommends the parentage panel consisting of 88 autosomal SNPs, developed by the International Sheep Genomics Consortium. However, selection of SNPs, which were included into the panel, was performed on the base of DNA profiles of North American, Australian and New Zealand sheep. There were no Russian breeds in these researches, and the possibility of applying ISAG panel to parentage testing of these sheep must be studied. We have performed the whole genome SNP study in four local Russian sheep breeds — Romanov (ROM, n = 22), Baikal’s fine-fleeced (ZBL, n = 7), Buryat sheep Buubey (BUB, n = 15), and Tuvan short fat tailed (TUV, n = 16) using Ovine SNP50k BeadChip. Data were processed for the total number of markers (54241 SNPs) and for 88 autosomal SNPs, recommended by ISAG.