The name Jovianus as well as the construction process included the building materials of the church are mentioned on the inscription, placed on the west entrance and on the narthex mosaic pavement. The church was built on the ruins of a Roman Conservatory, in the center of the Roman Agora of Paleopolis and very close to the port of Alkinoos. As the inscription reveals, various materials,which is still obvious on churches’ walls,were used from the nearby ancient sanctuaries.
The church suffered repeated damages through the years and was destroyed and rebuilt several times by the dominators of the island. During 15th century there was a large Catholic monastery complex, dedicated to the Virgin Anafonitria. It was preserved for 15 centuries, but unfortunately it was bombed during World War II and suffered irreparable damages. Parts of its mosaics are exhibited in the Byzantine Collection of Corfu housed in the Old Fortress. Located on the south side, there is the ancient agora, a vast outdoor space which used to be the political, religious and commercial centre of the ancient city.