The Greek Orthodox Church in Crete and across the Greek nation played an instrumental role in preserving the Hellenic identity during the Venetian and Ottoman occupation.

The Holy Metropolis of Kydonia and Apokoronou is headed in Chania city and includes the peripheral areas of Chania and Apokorana in the Chania prefecture. Christianity in Chania dates back from the 1st brought by Cretan converts favoring Judaism. During the first Byzantine period (330-825A.C.), the battle known as Iconoclasm between the iconoclasts and those favoring the icons led to the annexation of the Cretan Church to the throne of Constantinople. However because of the oppression coming from Constantinople, it gave leverage to the Arabs and the gradual Arabic occupation by the Saracens in 823-827A.C. leading to the Islamization of a big part of the population. The second Byzantine period, which was signaled by the reoccupation of the island by general Nikiforos Fokas in 961A.C. essentially, signaled also the reestablishment of Christianity and the reorganization of the Cretan Church by creating new parishes.

After 1204, a large part of Crete was occupied by the Genoese and by 1211 the Venetians had occupied the entire island. Despite their strong efforts, they failed at uprooting the Greek Orthodox Church. In the centuries that followed, the clergy in Crete was considered a place for opportunities, political rise and lobbying. Being a remote part of the Mediterranean, most clerks and priests were uneducated, ignorant and mostly corrupted. However the lay people of Chania resisted the Catholic doctrine and kept their fatherly heritage alive.

On the 22nd of August 1645, the city of Chania surrendered to Ottoman the siege. The conquerors confiscated public buildings, monasteries and private lands while demolished churches or turned them into mosques. The paradox lies in the fact that there was an agreement between the Ottomans and the Patriarch Church of Constantinople to set a Metropolitan of Crete that would have some powers practicing the Christian services and ceremonies as a tactic to have control over the enslaved Greeks. Most priests were respectable, courageous and inventive towards the Turkish demands, kept the Greek communities close and the Greek identity alive. While the Greek schools were shut down, the monasteries and convents that remained, gained power and wealth over time and replenished the loss of Greek education by providing books, organizing libraries and sustaining schools.

The Greek Revolution of 1821 against the Ottoman oppression, and the forthcoming years up to the beginning of the 20th century, the Cretan Church suffered great losses, material, financial but most of all among the clergy. Priests, bishops and Metropolitans were tortured, slaughtered and assassinated. In the dawn of the 20th century, Crete is liberated and the Cretan church reinvents and redefines its role and jurisdiction.