In Japan, amebiasis is domestically transmitted by two major populations: male homosexuals and mentally handicapped persons, which is remarkably different from most other developed countries where Entamoeba dispar infection is predominantly observed. Here we briefly summarize epidemiology of amebiasis in Japan. We also review our current understanding of the diversity of Entamoeba histolytica clinical isolates in Japan, based on polymorphic genetic markers, clinical representations, and in vivo virulence, using an animal model.