The Hepatozoon species in the myocardium of Japanese martens (Martes melampus melampus) was characterized by histological and molecular methods. Histologically, granulomatous nodules with Hepatozoon sp. merozoites/gametocytes, or schizonts, or both were observed in the hearts of Japanese martens. The most frequently observed forms were merozoites/gametocytes within phagocytes; each host cell included a zoite, which was not microscopically identifiable as a merozoite or gametocyte. Schizonts were oval in shape and 36.9 ± 5.7 × 28.9 ± 3.4 µm in size; each schizont had approximately 20–60 nuclei. The size of the merozoites could not be measured because no mature schizonts were observed. In the analyses of the partial 18S rRNA gene sequence, it was strongly suggested that the Hepatozoon sp. in Japanese marten and the Hepatozoon sp. in pine marten (Martes martes) in Scotland were the same species.