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The Church of St. John the Theologian is located near the Genoese fortress of Kafa. This small church was built in the style of a Roman basilica in the 14th century. It looks very ascetic, there is almost no decoration on the outer walls and inside the church, however, its location next to other ancient churches allows to feel the appearance of a medieval Kafa (modern Feodosia). 

On the hill above the Church of St. John the Theologian there are two towers of the Genoese Fortress of Kafa. Once this fortress was the largest in the Crimea, and the city of Kafa was one of the largest in Europe. Only two towers have survived from that fortress. An Armenian commune settled at their foot in the 14th century, which was later surrounded by a wall and called Ayots Berd (Armenian Fortress). Armenians built 5 churches inside this community, four of them have survived to this day.  

The largest of these churches was the Church of the Icon of Our Lady of Iveron. It has a cross-domed structure. According to the chronicles, it was built in 1385. There is no exact date when the Church of St. John the Theologian was built next door, but it is assumed that they were all built at about the same time. 

The Church of the Icon of Our Lady of Iveron used to be called the Church of John the Baptist. This name is still used today, so sometimes there is confusion with the names of two neighboring churches. John the Theologian and John the Baptist are different people. There is a large garden between these churches. There is a spring of water there, so many ornamental trees and flowers grow around churches.  

In front of the Church of St. John the Theologian there is a small courtyard surrounded by a high stone fence. A small stone bridge, also built in the Byzantine era, has been preserved nearby. The walls of the church and the fence are made of gray rubble stone. Nowadays, the Church of St. John the Theologian in Feodosia is closed to the public.