AbstractCurrent understanding of phylogeographical structure and genetic diversity of Siberian roe deer remains limited mainly due to small sample size and/or low geographical coverage in previous studies. Published data suggest at least two phylogroups: western (Ural Mountains and Western Siberia) and eastern (east from lake Baikal, including the Korean peninsula), but their phylogenetic relationship remains unclear. Combined sequences of cytochrome b (1140 bp) and the mtDNA control region (963 bp) were analyzed from 219 Siberian roe deer from 12 locations in Russia, Mongolia, and South Korea, which cover a large part of its range, to assess genetic diversity and phylogeographical status. Special emphasis was placed on the demographic history and genetic features of central, peripheral, and isolated populations. Results of median‐joining network and phylogenetic tree analyses indicate that Siberian roe deer from the Urals to the Pacific Ocean are genetically diverse and that geographical distribution and composition of haplogroups coincide with previously described ranges of the subspecies Capreolus pygargus pygargus and Capreolus pygargus tianschanicus. We found that peripheral populations in the northwestern parts of the species range (Urals), as well as the isolated population from Jeju Island, are genetically distinct from those in the core part of the range, both in terms of genetic diversity and quantitative composition of haplogroups. We also found that northwestern (Urals) and northern (Yakutia) peripheral populations share the same haplogroup and fall into the same phylogenetic clade with the isolated population from Jeju Island. This finding sheds light on the taxonomic status of the Jeju Island population and leads to hypotheses about the discordance of morphological and genetic evolution in isolated populations and specific genetic features of peripheral populations.