Genome Russia (GR) study is a national collaboration to expand our understanding of demographic history of peoples of Russia, to get deep insight into population genetics and to create a detailed genetic map of a country. Here we report analyses of matrilineal and patrilineal inheritance derived from whole genome sequencing data collected in the framework of the project. We examined sequences of 171 Y- chromosomes and 322 mtDNA ascertained from 14 ethnicities. We determined haplogroups for both Y-chromosomes and mtDNA sequences and estimated their distribution across the country. We performed phylogenetic and population genetic analyses for mtDNA and Y-chromosomes separately and then compared the results to reveal genetic history of indigenous groups living in Russia.