Mesowear analysis, one of the methods for reconstructing diets based on facet development on the occlusal surface of cheek teeth, has been applied mainly in extinct ungulates. To test how mesowear variables differ in same species from different habitats, this study investigated sika deer (Cervus nippon) from four localities (Urahoro, Nikko, Tsushima Islands, and Yakushima Island) in Japan. Data on two mesowear variables, ‘occlusal relief’ and ‘cusp shape’, were collected from buccal cusps of the left upper second molar. Several statistical analyses classified all the populations into their known food habits, except for the Yakushima population. These results suggest that mesowear analysis can roughly detect dietary position within the intraspecific spectrum from browser to grazer. However, specific dietary compositions or habitat conditions were could not be detected by the analysis. Therefore, care should be taken when discussing paleoecological conditions based only on mesowear analysis.