Sika deer, Cervus nippon yesoensis has distributed in Hokkaido, and been a critical agricultural and economical destructive mammals in decades. In southern Hokkaido area the deer populations have grown faster in this five years, and it might originate from Kyushu and Sikoku deer populations. However, it has never been unclear in detail. Therefore, we would like to identify the origin of sika deer lived in southern Hokkaido populations using fecal DNA analyses. We have collected 188 feces since 2009, and as a result of cyt b partial sequences analysis revealed that at least 6 samples of Matsumae Peninsula populations and a sample from Nanae population had a shared sequence with Kyushu and Shikoku deer populations. 10 samples of Kameda Peninsula populations shared with the eastern Hokkaido populations and 3 samples were established an original clade. We also have conducted light census surveys and recording analysis using infrared ray sensor cameras in order to monitor distributions and population dynamics. The frequency of recorded deer numbers were increased in Kameda Peninsula and remained static in Matsumae Peninsula. We will propose a maintenance and management plan of sika deer in southern Hokkaido area.