To the north of the Harbor Baths is the Church of Mary (The Council Church). The main entrance faces the Ephesus--Selçukkroad. The church was built dedicated to Mary and is an important structure in the history of Christianity. It was also the site of a Church Council in 431 AD.

The original structure was built as a Museion in the 2nd century and was 260 m long and 30 m wide. The building was a place for higher education in medical, as well as other sciences and for debates.