The church was erected in 1294/5 by Progon Zgur, a close relative of the Byzantine emperor Andronicus II Paleologos. The church added a nartex in the 14-th century and many other architectural features at later dates. It is well known as home to the earliest works, from 1295, of the painters Michael and Eutichios. In the 15th century, when the Turks pulled down St. Clement's church, the remains of the saints were transferred to this temple and since then this church has been known as St. Clement. When the sacred cathedral of St. Sofia was transformed into a mosque, St. Clement's church became the seat of Ohrid Archbishopric, which maintained its power under the Ottoman Empire and was even gain new territories under its jurisdiction. At that time, a lot of icons, the great Archbishopric Library with parchment handwritings from the 11th and 12th century, church pottery and other objects, as well as the oldest musical notations of Byzantine church chants were kept in the church. A monastery complex formed around St. Clement's temple, as well as an Archbishop's palace that burnt down in a fire in the 19th century. The frescoes in the church are divided in three zones. The first zone is over the altar and consists of body length archpriests, in the second zone are waste length figures of saints and the third zone depicts Tom's unfaithfulness, the Sacred Dinner and the Apostle's Purification. The church of St. Mary Mother of God is painted in the upper part of the apse. Some of the compositions painted in the deacon's room are "The Meeting of Mary and Elizabeth" and scenes from the life of St. John the Baptist. The frescoes in the proscomedia illustrate the life of St. Mary Mother of God. The Holy Warriors Dimitrius, George, Theodor Tiron, Theodor Stratilat and St. Prokopius and the great composition of the ascendance of Mary Mother of God is painted on the Western Wall. The third and fourth zone in the "naos" are painted with scenes from the life and sufferings of Jesus Christ.

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