The arrival of the Turks on Crete during the 17th century brought economic attrition and devastation to the island. It became an administrative unit of the Ottoman Empire, with Hándakas (Heraklion) as its capital and a number of regions ruled by a Pasha who was appointed by the Sultan. The Sfakiá region in the west enjoyed a special status. Venetian cathedrals and monastic complexes were converted to mosques and other facilities serving Islam; only a few monasteries remained to continue the copying of manuscripts. The cities and harbours fell into decay, large tracts of agricultural land were allowed to fall into disuse, the forests were decimated and little commerce was carried on. The local population was heavily taxed and oppressed, and a programme of obligatory conversion to Islam was vigorously pursued, often of whole villages. Conversion brought some relief from taxation, but refusal brought decimation to the population of a village. Some people submitted simply to survive, but maintained their old religion in secret. Those who resisted often fled into the mountains to form bands of fighters who were called Kléftes. The Sfakiá region was never conquered by the Turks, since the White Mountains and Samaria Gorge offered an impregnable refuge for resistance fighters.
 

From the beginning of the 19th century, the Cretans joined in the struggle for Greek independence. The Great Powers began to be actively involved and finally, in 1832, the Greek State was proclaimed after the withdrawal of the Turks from the mainland. Crete, however, remained under their yoke, passing first to the Egyptian Mehmet Ali and then -in 1840 - back under direct Turkish control. In 1866, at the Monastery of Arkadi near Rethymnon, several hundred Cretan men, women and children, led by the abbot, blew themselves up to avoid falling into Turkish hands. Inspired by their sacrifice, the Great Powers turned their attention towards the beleaguered island and finally occupied it, forcing the Turks to withdraw. Crete became autonomous under a Protectorate of the Great Powers, and Prince George of Greece arrived in 1898 to take control. However, only full union with Greece was acceptable to the people of Crete and Eleftherios Venizelos, from Thérisos near Chania, led an uprising in 1905 which resulted in the removal of Prince George. Venizelos became Prime Minister of Greece in 1910 and led the Balkan War of 1912 against the Turks. The Treaty of London gave the eastern Aegean, Epirus, Macedonia and Crete to Greece; in 1913, the union of Crete with Greece became a reality!