Construction of the Church of the Merciful Icon of the Mother of God began in 1889 in honor of the coronation anniversary of Emperor Alexander III. It was completed in 1898. The decision to build a church was made by the Maritime Department, which was the Ministry of the Military Fleet of the Russian Empire. Therefore, the church was built not far from the sea, at the Galernaya Harbor.

Such the location played a key role in the fate of the church during the Soviet period. Immediately after its closure in 1932, the building came under the jurisdiction of a diving squad. In the very center they installed a pressure chamber for diving training followed by a swimming pool. This resulted in complete destruction of interior of the church. By the end of the twentieth century, the general condition of the building became critical. The church was transfered the Russian Orthodox Church happened only in 2012. Since 2015 it has been closed for restoration.

The church project, created by Vasily Kosyakov, is made in the New Byzantine style. The unique appearance of the church features unusual embodiment of the five-domed system. The four side domes only protrude halfway from the central one. Under the drum of each of the domes there is a chain of arched windows passing into each other.