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This paper explores the historical construction of stigmatization toward Zainichi Koreans in Japan, as well as the consequences of such stigmatization. Zainichi Koreans are a minority group of ethnic Koreans living in Japan as special permanent residents, a unique identity formed as a result of the history of Japanese war imperialism and post-war nationalism. Zainichi Koreans have been residing in Japan for many generations now, and are no different from Japanese except for their ethnicity, or lack of Japanese blood. The homogeneity of Japan that boasts of pure Japanese blood is constantly conflicted by the long-term presence of Zainichi Koreans, which not only is one of many other ethnic minority groups that has been eroding that highly-sought-after homogeneity but is also a remnant of Japan’s history as aggressive colonizers. This conflict results in the stigmatization of the Zainichi Koreans, which is defined as a historically constructed process through which a person or group of people are seen as threatening the status quo of the society. This stigmatization can be explained by the system justification theory as well as the status characteristic theory, and is present in two aspects, namely structural, as well as intergroup stigmatization. Both posing unique sets of challenges and negative consequences to the Zainichi Koreans.