In 1549, Fransico Xavier (1506–52) landed in Kagoshima; with him, he brought Christianity.
As a Jesuit missionary, Xavier had great success. Xavier arrived at the beginning of the last decade of a century of civil war that had left the Japan in economic disarray. Christianity, as well as trade relations, spread with the support of Spain and Portugal. Many ports or places of trading, such as Nagasaki, were hotspots for Christianity. This intertwining of trade and religion led to the spread of Christianity and the influence of the Jesuit presence.
Fearing a repeat of colonization that occurred in other countries, Oda Nobunaga (1534–82) expelled foreign missionaries. Toyotomi Hideyoshi (1536–98) ordered the crucifixion of all Christians in Kyoto. The order only resulted in the martyrdom of 26 Christians that occurred in Nagasaki. These events forced missionaries to work more secretly.
When Tokugawa Ieyasu (1542–1616) became Shogun in 1603, he used the missionaries for their connections to the silk trade. Once the missionaries were circumvented, the daimyo were ordered to kick all of the foreign missionaries out through the port of Nagasaki and to destroy all churches. Japan entered a period of almost complete isolation from the West, with the exception of contact with the Dutch who were living on Dejima, a man-made island in Nagasaki. The next major event in Christian history in Japan was the Rebellion on the Shimabara peninsula. The rebels were Christians who had been enduring economic hardships and heavy taxation. Even though the rebellion was not entirely religiously motivated, the government feared a larger Christian uprising and used its forces to crush the rebellion.
With these and other forms of persecution occurring, many Christians went underground and continued to practice the Christianity they had learned. Although some synthesis and evolution occurred, much of the original Christians practices were retained by the Kakure Kirishitan (Hidden Christians). To this day the prayers can be recited that have been passed on and remembered for generations, what has been lost to these peoples is the meaning of the words. When Japan was opened again in 1854, Catholics sought out the Christians that had held onto their faith and practices in remote regions. Some Christians rejoined the Catholic Church and others remained separate. It is these groups of people and their history that we have studied, and that are the content of this site.