A number of attractive Turkish mosques (tzami) still survive in the city of Rethimnon. The Neratze Mosque used to be the church of Santa Maria. It has the best-preserved minaret in Rethimnon. The Veli Pasha Mosque has also been built on top of a church (Agios Onoufrios) and displays some unique structural features. The Kara Musa Mosque and the Ibrahim Han Mosque (converted Venetian cathedral) are also noteworthy.

The Janissaries Mosque is in the harbour of Chania and was constructed in 1645 when the Turks captured the city.