This church (formerly known as the Church of St. Nicholas or Aya Nicola Kilisesi) is an important mid-Byzantine-Era building, even though nothing of the original remains. The first temple on the site was built for the mother goddess Artemis, but collapsed in an earthquake in the 2nd century. A Byzantine church was built over the remains of this temple, but repeated raids and numerous earthquakes destroyed the church several times. The two domed chambers were part of a 5th- or 6th-century reconstruction and form the foundation for the domed church that was later built in the 9th century. The basilica on the site today is a 1789 reconstruction using materials that date to the 8th century, and some of the early frescoes are still visible. The honeycombed mosaic stones are originals and remain surprisingly intact, as do the domes forming the roof.

Speculation continues on which, if any, of the marble sarcophagi is the one belonging to St. Nicholas. We do know the date of his death and that his body was put in a Roman sarcophagus in the central apse on the south side of the church but was believed to have been moved after the Italian and Arab raids. The one in the west apse is believed to be that of the saint because of the reliefs of seagulls and fish scales (St. Nicholas is patron of sailors), but nobody knows anything for sure except that he's escaped to the North Pole.