Seasonal migration between the summer and the winter ranges was often observed in the Cervidae family. It is also observed for female sika deer in Hokkaido. To know the relationship between seasonal migration and spatial genetic structure of a population, we compare the genetic features among the eastward migrants, the northward migrants and the residents (no migrate) in the sika deer ( Cervus nippon ) population of eastern Hokkaido, Japan, based on mitochondrial DNA and microsatellite. In the results on mitochondrial DNA and microsatellite, the northward migrants showed higher genetic differentiation with the residents, whereas eastward migrants did not show the significant genetic differentiation with the residents.