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The Byzantine Empire and Orthodoxy were two powers which left their indelible mark on the historical course of Crete. In Chania alone more than 300 Byzantine churches are preserved. The early - Christian Basilicas of Sougia and the Basilica of Almyrida, with the exquisite mosaic floors, the Rotonda or the Church of Archangel Michael (6th century) in Episkopi, Kisamos,with its impressive and unique architecture and more than five layers of iconography, the Church of Agios Nikolaos (11th century) in Kyriakoselia in Apokoronas, the Monastira or Panagia Zerviotissa (12th century) in Stylos and the Church of Agios Georgios (1243) in Alikianos whose iconography is ascribed to Pavlos Provatas (1430) are some of the most significant ecclesiastical monuments of the prefecture.

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The church of Agios Georgios (1314) in Komitades, Sfakia, The Mother of God in Kakodiki of Selino, Archangel Michael (14th century) in Aradena of Sfakia and in Sarakina of Selino as well as a dozen more churches and chapels will not only draw the attention of the visitor but will also move him. Monasteries have existed on Crete since the 1st Byzantine period before 824, but in the 16th century, when under the Turkish threat, new monasteries were built and the existing ones were restored under the auspices of the Venetian conquerors.

The most important ones can be found in Akrotiri. There is the monastery of The Holy Trinity or Tzagarolon (17th century) which was greatly influenced by western architectural elements, a little further down the monastery of Gouverneto, dedicated to the Lady of the Angels (16th century), which stands before us in the shape of a fort and from there through a gorge the "Katholiko" of Agios Ioannis the Hermit (17th century), which is of special architectural interest as it has been adapted to the wilderness and impenetrability of the landscape, comes into view.

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Of equal importance are the monasteries of Panagia Odigitria or Gonia in Kolympari (17th century), the monastery of Agios Ioannis Theologos in Stylos of Apokoronas, the fortified monastery of the Virgin Mary Chrisoskalitsa on the western coast of the island which is built on a rock, the women's monastery of Chrisopigi in Mournies, Agia Kiriaki in Varipetro and the monastery of Agios Georgios in Karidi (12th century) to name but a few. The countless conquerors of this land have left their ineffaceable mark all over the prefecture with monuments, which recall the ordeal of the Cretan people but also its bravery.