History of the Church of Japan
The Church of Japan is an autonomous Orthodox church, whose primate is confirmed by the Church of Russia.
St. Nicholas of Japan (baptized as Ivan Dimitrievich Kasatkin) brought Orthodoxy to Japan in the 19th Century. In 1861 he was sent by the Church of Russia to Hakodate, Hokkaido, as a priest to a chapel of the Russian consulate. Though the contemporary Shogun's government prohibited the Japanese conversion to Christianity, soon some neighbors who frequently visited the chapel. In April 1868, among them three converted -- Nicholas's first three converts in Japan. While they were his first converts in Japan, they were not the first Japanese to do so—some Japanese who had settled in Russia had converted to Orthodoxy.
Apart from brief trips, Nicholas stayed in Japan, even during the Russo-Japanese War (1904-1905), and spread Orthodoxy nationwide, being appointed as the first bishop of Church of Japan. Nicholas founded the Cathedral of Tokyo in Kanda district and spent over fifty years of his life there; hence Holy Resurrection Cathedral (Tokyo, Japan) was nicknamed Nikolai-do by Kanda citizens.
The early mission to establish the Japanese Orthodox Church depended on the Russian Orthodox Church, especially in financial matters. The war between Russia and Japan created a politically difficult situation for the church. After the Bolshevik Revolution, the Japanese government had new suspicions about the Japanese Orthodox Church, in particular, that it was used as a cover for communist Russian espionage. The second bishop of Japan, Metropolitan Sergius (Tikhomirov), suffered severely from such governmental suspicion, and he was forced to resign his episcopacy and died under strange circumstances on August 10, 1945, five days before the end of the war. The Russian Church similarly suffered from Stalinist policy and had no ability to help the young church in Japan.
During the Fifteen Years War (1930-1945), which from 1939 to 1945 was part of World War II, Christianity in Japan suffered under severe conditions, the Orthodox Church especially. As early as the last years of Abp. Nicholas' life, the church administration considered consecration of a Japanese to the episcopacy. While over the following decades various candidates were considered, none were formally nominated for various reasons. The situation for the church changed in 1939 when the Diet of Japan enacted legislation requiring government registration of churches. The registration process meant foreigners could not serve in positions of authority within the church, although the legislation itself did not prohibit non-Japanese from such positions. Throughout 1940, the church leadership divided over how to satisfy the law, and Metr. Sergius was "retired". As the factions endorsed various candidates, one group had approached representatives of Russian Orthodox Church Outside of Russia (ROCOR), and quickly elected the Archpriest John Ono for consecration as a bishop. Fr. John and his wife Vera traveled to Manchuria where both took monastic vows and Fr. John was consecrated bishop with the name Nicholas on April 6, 1941. The disagreement between the two major factions continued throughout the war. 
After the Japanese surrender, the Allied occupation had a generous attitude to Christianity, given its predominantly American composition. Control over the Church of Japan by the Soviet dominated Church of Russia was forestalled by the Supreme Commander of the Allied Powers through the efforts of Colonel Boris T. Pash, who was the son of Metr. Theodosius (Pashkovsky) of the American Metropolia. As the majority of the Slavic- and Greek-Americans would attend local Orthodox parishes, Orthodoxy in Japan took a step forward. During the war, the Japanese Orthodox Church had almost no foreign contact. After the war, instead of the Russian Church, the American Metropolia, the precursors of the Orthodox Church in America (OCA) helped re-establish the Japanese Orthodox Church, and since 1946 Archbishops appointed by the American Metropolia ruled the Church of Japan. In that time, several youth who studied at the OCA's St. Vladimir's Orthodox Theological Seminary in New York are now the leaders of Japanese Orthodox Church. While a minority, under the leadership of Bp. Nicholas aligned itself with the Moscow Patriarchate, and were known as the "Russian Podvorye Orthodox Church in Japan".
Later, as the situation of the Russian Orthodox Church improved, the Japanese Orthodox Church came under the leadership of the Church of Russia again. In 1970 Nikolai Kasatkin was glorified by the Patriarch of Moscow and is recognized as St. Nikolai, Apostle to Japan. His commemoration day is February 16. In 2000, the Russian Orthodox Church glorified Bishop Andronic (Nikolsky) as a saint and martyr. He was appointed the first bishop of Kyoto and later martyred as the archbishop of Perm during the Russian Revolution.
Today the Russian Podvorye and the Church of Japan are reconciled and in so good terms that the former remembers both Patriach Alexey II and Metropolitan of All Japan in their liturgy, and that they commemorate a molieben in honor of St. Nikolai on his feast day.