The Church of Mary is a very long and narrow structure that was built in the late fifth-century. It was built over the southern stoa of an older Imperial Complex (Temple of Hadrian Olympios/Olympieion) and thus it is long and narrow. On the west was an atrium that measured 140 x 82 ft. To the east of that was a transverse narthex and to the east of that a long three-aisled church hall that measured 240 x 95 ft. with an apse on the east end.
After the earthquake in AD 557, it was rebuilt and the long central church was divided into two churches. The latest rebuilding was in the seventh century but St. John's Basilica became the focal point of worship in the region. In the middle ages, the area was used as a burial ground.