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The spread of Christianity in Japan brought negative impact to the government and people of Japan. It was started in 1549 when the Government considered Christianity as negative religion due to aggressive priests who destroyed Shinto and Buddhist shrines.Their acts had made military government (bakufu) to ban Christianity movement in Japan and sentenced Christian people and priests to death. The political and economic instability in the people and the rejection of bakufuto Christianity movement had triggered a rebellion in Shimabara. The revolt of Shimabarawas actually not based on religion sentiment, but the action to quell the rebellion had killed most Christians in Japan, while the remaining Christians in Japan formed kakurekirishitan (Silent Christian). Based on series of event, the research was focused on the policy made by bakufu to prohibit the Christianity in Japan.