We satellite-tracked Whooper Swans Cygnus cygnus wintering in northern Japan to document their migration routes and timing, and to identify breeding areas. From 47 swans that we marked at Lake Izunuma-Uchinuma, Miyagi Prefecture, northeast Honshu, and at Lake Kussharo, east Hokkaido, we observed 57 spring and 33 autumn migrations from 2009-2012. In spring, swans migrated north along Sakhalin Island from eastern Hokkaido using stopovers in Sakhalin, at the mouth of the Amur River and in northern coastal areas of the Sea of Okhotsk. They ultimately reached molting/breedmg areas along the Indigirka River and the lower Kolyma River in northern Russia. In autumn, the swans basically reversed the spring migration routes. We identified northern Honshu, eastern Hokkaido, coastal areas in Sakhalin, the lower Amur River and northern coastal areas of the Sea of Okhotsk as the most frequent stopover sites, and the middle reaches of the Indigirka and the lower Kolyma River as presumed breeding sites. Our results are helpful in understanding the distribution of the breeding and stopover sites of Whooper Swans wintering in Japan and in identifying their major migration habitats. Our findings contribute to understanding the potential transmission process of avian influenza viruses potentially carried by swans, and provide information necessary to conserve Whooper Swans in East Asia.