This study analyzed the process by which the boundaries of Japanese were newly defined in the repatriation phase immediately after the defeat of Japan through the maritime quarantine, which has not received much attention so far. On August 15, 1945, with the collapse of the empire, Japan was forced to undergo a drastic change in the boundaries of its members from a multi-ethnic empire to a monoethnic nation-state. This change surfaced in the process of repatriation in the form of inclusion of Japanese overseas and exclusion of foreigners living in Japan, and the repatriation port was the center of this change. As a result of the analysis, it was found that the repatriation of Japanese overseas was carried out under strong caution against infectious diseases, especially the influx of cholera. However, because they were the subject of inclusion, GHQ/SCAP and Japanese government mobilized many resources to place them inside the territory in a way that did not disrupt Japan. On the other hand, in the case of foreign residents in Japan, maritime quarantine was initially carried out in a limited manner with the aim that their existence would not be an obstacle to the repatriation process of Japanese overseas. However, as the number of returnees to Japan increased, especially among Koreans, the thorough exclusion began with the support of the ‘scientific basis’ to prevent the influx of cholera. And this maritime quarantine against stowaways centered on the repatriation ports was the beginning of the process of positioning colonials, whose the legal status was still vague, outside the boundaries of the Japanese. The maritime quarantine conducted at Japan's repatriation port immediately after the defeat examined in this study is one of the cases that clearly shows the political nature of quarantine by focusing on the structural change from the empire to the nation-state.