By signing the Treaty of Shimoda in 1855, the government of Japan committed itself to providing land and housing for the Russian Consulate and by the Treaty of 1858, the right of permanent residence in Japan was granted for Russian diplomatic representatives. Then the first Consulate of the Russian Empire was opened in Hakodate.
Late in 1858, the first mission of the Russian Consulate, led by Iosif Antonovich Goshkevich arrived in the Japanese city of Hakodate. The Russian mission was temporarily housed in the local Buddhist temples. The Consul, I. A. Goshkevich immediately started negotiations with the Japanese authorities to allocate a plot of land for the mission. Finally, they agreed to allot land in the coastal zone on the foothills of Mt. Hakodate, where is the present location.
In 1860 a two-story consulate building, four one-story buildings for accommodating the Russian families and an orthodox church attached to the consulate were first built on this land. A priest Vasily Makhov, who arrived in Hakodate in 1859, did not remain for long. In 1861 Priest Nikolai, who was later canonized for his activities in Japan as St. Nikolai of Japan was sent after Makhov. St. Nikolai became the first priest who conveyed the Orthodoxy to Japan.
In the same land they also built an elementary school, a sewing school for girls and a hospital, which had contributed to the development of the education and medical treatment for Japanese. Officers of the consulate gladly taught people medical technology, photography, sewing, baking and other art of living to the people in Hakodate.
The Russian Consulate staff moved to Tokyo in 1872 and the church was transferred to the Orthodox Church in Japan. At the same time St. Nikolas established a base in Tokyo to begin his missionary work throughout Japan.
The current Hakodate Orthodox Church was constructed as a replacement for a wooden church that had burned down in 1907. It was completed in 1916 and is an iconic example of Russian Byzantine architecture, with brick and white-plaster walls, green copper roofs, and an octagonal bell tower. It was consecrated by Metropolitan Sergius (Tikhomirov), who was a successor of St. Nikolas. The church itself and the iconostasis were designated Important Cultural Properties in 1983 and the bell’s sound the 100 Soundscapes of Japan in 1996. In 1985-1988 and 2021-2023 the church was restored on a large scale, which included the earthquake-resisting work.