New data on the variants of the B-chromosome system of 8 individuals of Korean field mouse A. peninsulae caught in 2016 in the Irkutsk region in vicinity of Sarma settlement on the western shore of Lake Baikal are analyzed. In addition, the karyotype of a single female of the Korean field mouse caught on the Vitim Upland has been studied. As a result of analysis of frequency and morphotypes of the B-chromosomes of 83 individuals of the A. peninsulae from 10 points of its range in the Baikal area are shown they belonging to different geographic populations. Interpopulation differences were determined by the variability of 0–4 macro-B-chromosomes and 0–11 micro-B-chromosomes. Especially significant differentiation in karyotype in mice is observed between western and eastern coast of Lake Baikal. The similarity of karyotypes and B-chromosome systems in representatives of A. peninsulae in two geographically remote locations (southern coast of Lake Baikal and the Vitim Upland in Transbaikalia) apparently indicates the importance of stochastic processes in the formation of various B-chromosome systems of the Korean field mouse. The revealed clinal variability in the frequency of invividuals with micro-B-chromosomes and the variability of the number of micro-B-chromosomes in individuals from remote samples of this region will allow us to reveal the directions of A. peninsulae migration within postglacial period.