At the heart of the site stands the Monastery of St. Mary, dating from 13 -14th centuries AD. The Monastery of St. Mary represents the medieval period and is composed of the Church and Refectory.


The church, built between 1250-1270 upon the remains of an older church, is unique in Albania owing to the unusual configuration of its cruciform shape and was built in part from spolia from the ancient theatre. Its echo-narthex contains a Doric column drum from the Temple of Shtyllas, currently being used as a well cover, and the remains of a 14th century fresco of great historical importance. An inscription on the left side of its west wing evidences that it was reconstructed by the Byzantine Emperor, Andronicus Palaeologus the Second. Below the inscription there is a painting of the emperor's family, which features eight people in regal ceremonial dress. Another inscription on a stone slab found at the bottom of an outer southern wall of the chapel, bears the date 31 March 858. The whole interior of this chapel built in the Byzantine style was once covered in paintings. The church features the first four icons of the iconostasis. Here and there on the surrounding walls one can see bas-reliefs of the ancient town of Apollonia. The chapel is dedicated to the Assumption of Our Lady, Saint Mary, celebrated on the 15th of August each year, day in which a regional fair is held in the area.


The surrounding monastic complex, defensive wall and bell tower, date from various points in the history of the monastry, from the 13th to the 20th century. The cells of the monks were located in the north and west sides; on the southern side is the bell tower, reconstructed at the beginning of the 20th century; the east side is closed by a defensive wall, and the remainder of the west side contains the refectory and the toilets.


The refectory is a long triconch shape and dates to the early years of the 14th century. It boasts some of the most complete medieval frescoes surviving in Albania. The entrance to the monastery is by a monumental entrance with a double wooden door also on the west side.


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