The church was built around AD 520 on the foundations of an older Christian church where Nicholas had served as bishop. It is described as an East Roman basilica of Byzantine character, and Justinian I contributed to its reconstruction. The article names no architect and gives no materials or dimensions. The sarcophagus is thought to be the original burial place. His remains were moved to Bari in 1088, or 1087 by the text. Flooding and silt later filled the church.
Nicholas I of Russia restored it in 1862 and added a tower, which altered its Byzantine character. Orthodox use ended in 1922 or 1923 when the local Greeks left in the population exchange. Excavations began in 1988.
The wall frescoes include a cycle on Nicholas's life. It is now a museum, on UNESCO's tentative list, and the Orthodox liturgy is celebrated there occasionally on December 6.

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