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The Metropolis comprises the provinces of Kydonia and Apokoronos, in the Prefecture of Chania and its See is in Chania. Kydonia was one of the oldest and most important cities on Crete. Its diocese, like most on the island, was funded by St. Titus. It was founded even before 381 AD, since Bishop Kydoios attended the 2nd Ecumenical Council (Synod). Arab invasions ruined most island metropolises and one of them was the Diocese of Kydonia.

During Venetian rule, the Orthodox church declined, while under the Ottomans, the diocese used as its Catholicon church the only Orthodox church, namely that of Agioi Anargyroi (Holy Unmercenaries).

In the 19th century a new Catholicon was built, dedicated to Mother Mary’s Presentation (Eisodia tis Theotokou).
The diocese was raised to the level of a metropolis by decision of the Ecumenical Patriarchate 1962. Its Metropolitan is Mr. Damascenus, with 106 parishes, 123 priests and 6 Monasteries under his jurisdiction.