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The Japanese had issues with Christianity because the religion went against everything Japanese.  It was highly structured and focused belief on a single divine figure, rather than many spirits found in nature (kami) and very different from the Buddha.  The missionaries were also threatening because of the new world they brought with them.  Access to European goods, including military equipment, was threatening to the central government because powerful daimyos could usurp the power of the central regime.

Hideyoshi died in 1598, and thus began the Tokugawa Shogunate (1600) under Tokugawa Ieyasu.  The Tokugawa held approximately one quarter of the agricultural land in Japan.  They also administered Kyoto, Osaka, and Nagasaki, as well as several other smaller cities.  Under the Shogunate, there existed a system of daimyos.  Two types of daimyos served the Shogunate: fudai (hereditary) and tozama (outsiders daimyos.)  The fudai had pledged loyalty to the Shogunate before 1600 and were thus raised to higher status after Sekigahara gained control.  These daimyos were allowed to serve in the shogunal government.

The tozama daimyos, on the other hand, were not allowed to participate in any aspect of the Edo central government.  The daimyos remained rulers of their regions (han) but most importantly adhered to a Tokugawa system named sankin kotai.  This system, literally meaning alternate attendance, required that daimyos spend approximately half their time at the shogunal court in Edo and the rest of their time at their han.  This system left their families in Edo when they returned to their regions.  This system was also thought to dissuade any seditious thoughts because the daimyos would always have their family in Edo.  Also, the financial burden this �commute� inflicted on the daimyos meant that they would have less resources should they ever choose to oppose the shogunal court.

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Tokugawa Ieyasu withheld on attacking the missionaries, even though the laws against missionaries were still in effect from Hideyoshi.  Ieyasu did this initially in an effort to increase trade with the British and Dutch.  In 1614, feeling that the foreign missionaries were engaged in subversion, issued an edict that strictly banned Christianity.  This edict led to the mass persecutions of over 6000 European and Japanese Christians until the killings subsided in 1640.

The Tokugawa period brought an increased interest in Confucianism.  This period saw the decline of Buddhism and the beginning of zealous study of Confucian texts, along with application of Confucian principles in Japanese society.  Neo-Confucianism evolved in Sung Period China by Chu Hsi (1130-1200) and this was the practice that was most popular in Japan.  Tokugawa Shogunate found Chu Hsi's Neo-Confucianism as doctrinally orthodox.  Neo-Confucianism bases itself on a philosophy of reason or principle.  There was a stress on historical research which spurred a revival in learning during the Tokugawa period.  However, with all this emphasis the strongest point of Neo-Confucianism was a concentration on conduct of affairs of men now, not then.  Neo-Confucianism was most heavily advocated in Japan by Hayashi Razan (1583-1657.)  Razan was the chief force advocating Chu Hsi�s Confucianism to the shogunal court, and his family became the authority on Confucian scholarship in Japan. 

The Tokugawa period also saw an increase and expansion of commerce, especially domestically.  A bourgeois culture developed in and around large cities like Osaka and Edo.  This flourishing culture can best be seen in the Genroku cultural epoch, which effectively lasted from 1675-1725.  Genroku explained the growth of a townsmen-oriented culture that ensured over fifty years of peace and commercial growth.  The merchant class began to grow and gain authority in Japan.  Still labeled inferior by the samurai classes, merchants were beginning to progress by asserting social and cultural independence.

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