Why did the Shogun isolate Japan?
The Tokugawa Shogunate was concerned over the rise of Christianity and other Western influences brought by the Portuguese Trade. The Shogun isolated Japan from Western but not Eastern trade.
The Tokugawa Shogunate established in 1600 by Tokugawa Ieyasu. He was informed of the chaotic situation in the Philippines caused by Western influences. He caused the isolation of Japan from except for a small island near Nagasaki for trade. As well he caused the persecution of Missionaries in Japan to eliminate the influence of the Religion.
Japan's isolation continued for the next 250 years until Admiral Perry came to Japan.