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The general Nikephoros Phokas regained control of Crete for the Eastern Roman Empire in 961 under whose administration it would remain until the Venetian invasion of 1204. Candia remained the capital of Crete and became the seat of the Archbishop of Crete. Under the administration of the Ecumenical Patriarchate, the church on Crete was designated a [[metropolis]] with its head a [[Metropolitan]] who was over twelve bishops. A new [[cathedral]] was built in Candia, dedicated again to the Apostle Titus. The site of this cathedral is believed to be that on which the present day Church of the Apostle Titus is located. The names of Elias in the eleventh century, John in the twelfth century, and Nicholas are mentioned as metropolitans. With the Venetian occupation of 1204, Nicholas fled to [[Nicea]], with bishops Gregory of Petra and John of Arcadia. Bishop Paul of Knossos and the unidentified bishops of Herronissos and Agrion remained on Crete.
The Venetian occupation of Crete lasted from 1204 to 1669. During this time the ecclesiastical state of affairs changed radically. The Venetians exiled the Orthodox hierarchs and reorganized the church on the Latin model as an archdiocese with an Roman Catholic archbishop and bishops[[bishop]]s. While the new hierarchy attempted to convert the populous, they remained firm in their Orthodox faith even without Orthodox bishops. The Orthodox faith was sustained by the many [[monastery|monasteries]] with their [[abbot]]s and simple [[clergy]] in the villages and towns.
As the Venetians prohibited the presence of Orthodox bishops on Crete, the Ecumenical Patriarchate maintained the position of the archbishop as ''displaced'', that is outside the physical borders of his jurisdiction. In this manner a continuity was kept. Among the displaced bishops were the Cretans Nikiforos Moschopoulos, in late thirteenth century and Anthimos, the metropolitan of Athens, both who bore the title of “president” of the Church of Crete.
The Turkish occupation of Crete that began in 1645 altered again the ecclesiastical state of affairs on Crete. Among the first acts of the Ottoman government was placing the Christians under the authority of the Ecumenical Patriarchate that was responsible to the Sultan for the actions of the Christian community. Neophytos Nikousios, who was a monk at the Monastery of Arcadi, had been consecrated Metropolitan of Crete in 1647 and was active in Crete under Turkish rule as the first Orthodox prelate after the long period of domination by the Venetians.
The oldest documentation concerning the organizational structure of the Metropolis noted that it had twelve bishoprics that maintained their historic names: Gortyna, Knossos, Arcadia, Herronissos, Avlopotamos, Agrion (Rethymnon), Lambi, Kidonia, Iera, Petra, Sitia, and Kissamos. During the Turkish occupation the number of bishoprics varied from ten to twelve. The metropolitan was noted to have an [[vicar|assistant ]] bishop before 1821 whose title was Diopoleos. In 1700, the metropolitan gained a new title, that of ''…of Crete and All Europe''. The area of his [[see]] covered that of ancient Gortyna and the province of Sfakia.
Other than the administrative problems caused by Turkish rule, the lack of a [[cathedral ]] was of importance to the Metropolis. Under Turkish rule, the Church was allowed only one [[church ]] in Candia (Heraklion), that of St. Matthew. St. Matthew was a dependency of the [[monastery ]] of [[St. Catherine's Monastery (Sinai)|Sinai]], a relationship that was not well. Without a cathedral, the metropolitan was forced to travel among the churches and monasteries. Against this state of affairs Metropolitan Gerasimos Letitzis was able, after a difficult struggle with the Turkish authorities, to have the small Church of St. Minas built as his cathedral. The church was consecrated on [[November 10]], 1735, but was not acknowledged officially until an ecclesiastical act on [[June 19]], 1742. The small cathedral became the center of the Christian community in Heraklion. Over the years the cathedral was adorned with icons. In 1800, Metropolitan Gerasimos Pardalis brought to the cathedral six large icons [[icon]]s from the Monastery of Vrondissi that were painted by the renowned Michael Damaskinos.
During the period of Turkish rule, the Ecumenical Patriarchate used its position within the Ottoman empire to help the Church in Crete by bringing many of the monasteries under the protection of the Patriarchate as stavropigial institutions. This practice began under the first metropolitan under Turkish rule, Neophitos Patellaros, who from 1654 transferred many of the largest and most wealthy monasteries including Arcadi, Arsanios, Holy Trinity of Tzagarolon, Holy Virgin of Gdernetos, Chrissopigis, and Jerusalem of Malevizi.
As agitation for Greek independence gained popular support, the people of Crete revolted against the Turks. In retaliation on [[June 24]], 1921, the Turks conducted a massacre in Herkalion that is remembered by the populace as ‘’o megalos arpentes’’ (the great ravage). Among the victims were Metropolitan Gerasimos Pardalis, and five of his bishops: Neofitos of Knossos, Joachim of Herronissos, Ierotheos of Lambis, Zacharias of Sitia and Kallinikos, and the titular bishop of Diopolis. The [[see ]] of metropolitan remained vacant for the next two years until the sultan consented, in 1823, to the consecration of Kallinikos of Anchialos as the Metropolitan of Crete. At the same time the bishopric of Knossos was abolished and became part of the metropolis.
During the time of Metropolitan Meletios A’ Nikoletakis (1830 to 1834) the structure of the Metropolis changed greatly. Bishoprics were merged to make five bishoprics. In 1862, the bishoprics were re-established as before except that Knossos remained part of the metropolis. Later, Metropolitan Dionissios Chanritonides began construction of a new, larger Cathedral of St. Minas. This cathedral was completed and consecrated under the last metropolitan to rule under Turkish rule: Timotheos Kastringannakis (1870 to 1898). The consecration took place on [[April 18]], 1895.
