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Approximately 500–1000 White-tailed Eagles (Haliaeetus albicilla) each year winter in Japan. These include both residents breeding in northern Japan and migrants from regions farther north, such as the far-east of Russia. Collision with wind turbines has recently emerged as the primary cause of death for White-tailed Eagles in Japan and the negative impact of this increased mortality on the population is a matter of concern. Most collisions occurred during the wintering period in Hokkaido, the northernmost part of Japan, but the origin of the dead birds is currently unknown. Japanese resident population may be genetically different from the population in far east Russia, and an evaluation of the impact of mortalities from collisions on each subpopulation is required. Therefore, the purpose of this study is to examine the genetic differences among the regional breeding populations of White-tailed Eagles in Hokkaido and far east Russia, and to estimate the origins of dead eagles found at wind farms in Hokkaido based on genetic analyses. Mitochondrial DNA (mtDNA) haplotypes of the dead eagles were compared with the haplotype datasets from breeding populations in Hokkaido and in the four regions of far east Russia. Multilocus genotypes from nuclear DNA were also analyzed using assignment methods. The results of these analysis suggested that three different haplogroups existed within the mtDNA haplotype datasets and it was likely that the majority of eagles died in turbine collisions in Hokkaido originated from the Hokkaido breeding population.