During the Ottoman period the fortress acquired the name "Koules" by which it is still known. This name derives from the phrase "Su Kulesi" (sea fortress). Under Ottoman rule several alterations were made to the upper level of the fortress, involving the addition of crenellations, cannon emplacements and a small mosque. Part of the minaret attached to this, which replaced the earlier lighthouse, still survives in the northeast corner of the roof.

The upper level of the fortress with additions and alterations, 2003 (photograph: Vassilis Kozonakis)
View of the upper level showing battlements and casements, 2003 (photograph: Vassilis Kozonakis)