A parish temple located on the homonym district of Aghioi Anargyroi, which is recorded from 1583 in Venetian documents. Despite its small size, the district is represented in most of the city's images.

After the occupation of Chania by the Turks in 1645, it was the only Orthodox Church in the city until the 19th century and is now used as the headquarters of the Bishop of "Kydonia". Most of the activities of the Christian community were organized around the temple during the Turkish period, such as schools, charity organizations, the habitation of the Bishop, ect. Most of these impressive buildings are still preserved around the temple. The church consists of three parts, from which the southern is the most recent extension of the Venetian noble house, where the temple was initially incorporated and was probably a private chapel. 
The excavation works have revealed that the domed eastern part was built first. Later, an extension was constructed on the west side, and then a larger aisle was added on the north side. Finally, an extension was added to the south. Most of the decoration of the temple dates between 1837 and 1841, as indicated on the inscription of the wood-carven iconostasis.

During the recent preservation works, the initial inscription was uncovered, which records the names of the Venetian rector of Chania, Nicolaus Venerio and Georgios Stavrianos as dedicators.
The icons were painted in about 1625 by the monk Amvrosios Emporos from Chania and other painters of west Crete, are of particular interest.
The icons were dedicated by the Venetian officer and by the citizens to the new local Saint Aghios Ioannis the Hermit, asking for his protection from the Turkish threat.