The population of the sika deer (Cervus nippon) has been expanding and caused severe damage to the vegetation in Hokkaido, Japan. According to the increase in abundance, their distribution range has also expanded. Has the spatial structure of the population changed during the expansion? We investigated spatial genetic structure of this population using microsatellites (15 loci) and mitochondrial DNA (D-loop) for two periods (204 samples for 1991-1996 and 211 samples for 2008-2010). We used georeferenced multilocus microsatellite genotypes and mitochondrial DNA in spatially implicit (STRUCTURE) and spatially explicit (GENELAND) models to characterize patterns of landscape genetic structure. Preliminary results of GENELAND indicate the existence of 2 units (microsatellites) and 4 units (mtDNA) in 1991-1996, while 4 genetic units (microsatellites) and 4 units (mtDNA) in 2008-2009. Levels of genetic diversity of sika deer were very low in both two periods. These results suggest that the population structure significantly changed for over 15 years and potential barriers to the movement of male and female sika deer were different.