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The shogunate perceived Catholic Christianity to be an extremely destabilizing factor, leading to the persecution of Catholicism.
The Shimabara Rebellion of 1637 – 38, in which discontented Catholic Christian samurai and peasants rebelled against the bakufu — and Edo called in Dutch ships to bombard the rebel stronghold — marked the end of the Christian movement, although some Catholic Christians survived by going underground, the so-called Kakure Kirishitan.
Soon thereafter, the Portuguese were permanently expelled, members of the Portuguese diplomatic mission were executed, all subjects were ordered to register at a Buddhist or Shinto temple, and the Dutch and Chinese were restricted, respectively, to Dejima and to a special quarter in Nagasaki.
Besides small trade of some outer daimyo with Korea and the Ryukyu Islands, to the southwest of Japan's main islands, by 1641, foreign contacts were limited by the policy of sakoku to Nagasaki.

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