Simple SummaryThe role of hybridization in biological evolution and cases of hybridogenic speciation is one of the most complicated but also interesting and actively studied topics. Russet ground squirrelSpermophilus majoris known as a fine biological species according to a number of criteria—morphological, ecological, and behavioral, respectively. Nevertheless, a large body of evidence has accumulated on the hybridization ofS. majorwith four neighboringSpermophilusspecies. Our goal was to identify their contribution to the nuclear and mitochondrial genome ofS. major, and to propose a hypothesis describing the hybridization history in space and time. We found that 36% ofS. majorindividuals had extraneous alleles, and every contacting species contributed toS. major’s genetic variability. Our data suggested at least five independent hybridization events that were associated with shifts in the species ranges due to paleoclimate changes. Two of them were potentially accompanied by mitochondrial captures with replacement of the mitochondrial genome of one of the hybridizing species. We highlight the potential threat to the existence ofS. majoras a species under the current conditions of population decline along with the simultaneous influx of extraneous genes. It is also particularly important to emphasize the necessity of protecting this inhabitant of unique steppe communities.AbstractAmong the numerous described cases of hybridization in mammals, the most intriguing are (a) cases of introgressive hybridization deeply affecting the evolutionary history of species, and (b) models involving not a pair of species but a multi-species complex. Therefore, the hybridization history of the russet ground squirrelSpermophilus major, whose range has repeatedly changed due to climatic fluctuations and now borders the ranges of four related species, is of great interest. The main aims of this study were to determine the direction and intensity of gene introgression, the spatial depth of the infiltration of extraneous genes into theS. majorrange, and to refine the hypothesis of the hybridogenic replacement of mitochondrial genomes in the studied group. Using phylogenetic analysis of the variability of mitochondrial (CR,cytb) and nuclear (SmcY,BGN,PRKCI,c-myc,i6p53) markers, we determined the contribution of neighboring species to theS. majorgenome. We showed that 36% ofS. majorindividuals had extraneous alleles. All peripheral species that were in contact withS. majorcontributed towards its genetic variability. We also proposed a hypothesis for the sequence and localization of serial hybridization events. Our assessment of theS. majorgenome implications of introgression highlights the importance of implementing conservation measures to protect this species.