Isa bey Mosque was built in 1375 and represented the transition from Seljuk to Ottoman traditions. Designed by Ali, an architect from Damascus, it shows influence from The Great Mosque in Damascus.

The skilled Syrian artisans who built it used materials from the ruined Basilica of St John and the Temple of Artemis; indeed, the decaying classical city provided plentiful antique marble to adorn its walls. However, avoiding any show of Roman ornament, the details are entirely Islamic.

It was the first mosque in Turkey with a courtyard.

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