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The Church of Crete is an ApostolicEraChurch: the first Christian nucleus was formed here around 64 A.D. by St. Paul, during his 4th missionary journey. Paul assigned to his disciple Titus, who became the first Bishop of Crete, the systematic teaching of Christianity on the island. When Christianity expanded, the Cretan Church was organised with a Primus and Bishops, who made up the local Synod. The Primus of the Church of Crete held the title of Archbishop and Crete was one of the twelve Illyrian Archdioceses (Illyria was the name of the Balkan Peninsula at the time).
During the first Byzantine period, the Primus of the Church of Crete was seated in Gortys (present day Gortyna), the administrational centre of the island since the Roman period.
In the beginning of the 8th century, there were twelve of them and Crete was called ‘dodecathrone’, i.e. ‘having twelve sees’. Until that time, the Archdiocese of Crete was under the administrative see of Rome, but the iconomach emperors detached it and annexed it to the Constantinople See (around 754), because the Pope followed an iconophilic policy.
The Arab Period (around 824-961 A.D.) is a major turning point in the political and ecclesiastical history of the island.
After Nicephorus Phokas reconquered Crete in 961, the so-called second Byzantine period started for the island (961-1204). Now the political and religious centre was Candia, which also became the See of the Primus of the Church of Crete.
The Venetians removed the Orthodox Christian leaders of the church and named the Church of Crete an Archdiocese, following the Latin canon. They established a Latin Archbishop and Latin Bishops.Orthodoxy supported during those critical times by the active Father Superiors and scholarly monks at the numerous orthodox monasteries, as well as the ordinary priests of the villages and urban churches.
The Ottoman occupation period (1645-1898) changed, among other things, the state of religious affairs in Crete. One of the first political acts of the Ottoman administration was to restore the Orthodox Hierarchy of the Cretan Church. After 1700 the Cretan Metropolitan was given the title ‘Metropolitan of Crete and the whole Europe’, a title he still holds.
During those harsh times the Ecumenical Patriarchate helped the Church of Crete in various manners.
During the 1821 liberation struggle the Church of Crete was decapitated. In the mass slaughter of Herakleion on 24 June 1821, wildly furious Ottomans slew the Metropolitan of Crete and five bishops.
In 1862 the dioceses of Crete were restored, except of that of Knossos, which was abolished and annexed to the Metropolis.
The status of the Church of Crete was legally recognized by the CretanState in 1900. The Primus of the Cretan Church is elected by the Patriarchate in Constantinople and enthroned by virtue of a decree issued by the GreekState.

In 1962, an act of the Ecumenical Patriarchate stipulated that all Cretan bishops should receive the title of Metropolitan, while in 1967 the Metropolis of Crete was proclaimed an Archdiocese and the Metropolitan of Crete an Archbishop
(Source: Website of the Archdiocese of Crete).