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The former provinces of Rethymno and Mylopotamos comprise the Holy Metropolis of Rethymno and Avlopotamos. The first Dioceses of the region were first established in the 5th century AD. Minutes of the 3rd and 4th Ecumenical Council mention the Dioceses of Lampe and Eleftherna. Another Diocese located in an ancient city was the Diocese of Axios, which is also part of the Metropolis.

Sepulchral inscriptions from this era found in nearby villages and transported to the museum of Rethymno attest to the existence of the Dioceses.

Under Arab rule, the Metropolises of Rethymno and Avolopotamos were, like most other Metropolises, destroyed during raids. After the period of Arab rule, there were three Dioceses, namely of Kalamonas, Agrion and Avlopotamos. During the period of Venetian rule, all except the Diocese of Agrion were ceded to the Catholic Church. In 1838, the Dioceses were merged, with the new seat in the city of Rethymno.

In 1962, the Diocese of Rethymno and Avlopotamos was promoted into a Metropolis by order of the Ecumenical Patriarchate. It is currently headed by Metropolitan Eugenios.

The Metropolis consists of 101 parishes, 12 Monasteries and 118 clergymen.