As the number of sightings of Japanese sika deer (Cervus nippon) increases in Ibaraki Prefecture, Japan, male sika deer have recently appeared in Tsukuba City (2015 and 2016) and Yuki City (2019), located in the southwestern part of the prefecture (ISW). We analyzed the mitochondrial DNA control region sequences of three individuals and compared them with those of sika deer in the neighboring areas to infer their areas of origin. The three individuals shared an identical haplotype 6TCG1 and repeat motif TD-2. Pairwise FST and Exact Test suggested significant genetic differentiation in the Nasu-Yaita/Boso Peninsula/Kanto Mountains and ISW. Based on these results, the most possible area of origin of these deer was Nikko in Tochigi Prefecture, which was the only area with the identical haplotype-repeat motif “6TCG1-TD-2”. The areas where we obtained the three deer are all very close to the Kokai River, which originates in the Nasu area, Tochigi Prefecture, and the Kinu River, which has its upper reaches in Nikko and northern Tochigi Prefecture. The sika deer in ISW may have migrated from Tochigi Prefecture using the green areas along these rivers as corridors.
