Our research aim is that reveals genetical background of Japanese chipmunks, Tamias sibiricus lineatus distributed in Mt. Hakodate, Hokkaido. Also we show that the possibility of alien individuals invaded in native Mt. Hakodate population. Mt. Hakodate is a land-tied island and there are several unique and original flora and fauna. This mountain shaped 10,000 years ago and almost isolated from other areas because of its land-tied geological condition. We have collected over 144 feces of chipmunks in there and conducted DNA analyses using D-loop and cyt b partial sequences. As a result some samples of Mt. Hakodate had a shared sequence with Korean and China populations and those samples distributed whole areas of the mountain. Our results suggest that multiple invaded roots of chipmunks in Mt. Hakodate from Korea and China had existed, but on the other hand, some native chipmunks also had lived in there and it would be originated from about 300,000 years ago. We also conducted direct observation and recording analysis using infrared ray sensor cameras and estimated its home ranges. From these data we would like to establish a management plan to control native and invaded animal in natural situations.