The objective of the present study is to reveal the movements and genetic structure of bears in eastern Hokkaido, Japan, based on GPS telemetry data and mtDNA haplotypes. From 2009 to 2011, 16 bears were captured in Shibetsu town, and 8 males and one female were tracked. Males traveled to and from the Shiretoko Peninsula and the southern Nemuro region. On the flat land, bears moved through windbreak forests and riparian forests as movement corridors. We investigated mtDNA haplotypes for 23 males and 7 females using tissue samples obtained around Shibetsu town. All females were assigned to Cluster B, suggesting that Cluster B was distributed from the Shiretoko Peninsula to the Shibetsu region. On the other hand, males were assigned to either Clusters A or B, indicating that males born in the distribution area of Cluster A, the southern Nemuro region and central Hokkaido, have moved to the Shibetsu region. Therefore, the Shibetsu region is the boundary area of the distribution areas of Clusters A and B, which suggests important implications for maintaining the genetic diversity of brown bears as a boundary zone between Clusters A and B in Hokkaido.