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The Metropolis includes the provinces of the same name in the Prefecture of Chania and its See is in Kissamos, which was already an Archdiocese as early as early Christian times. The age of the Archdiocese is known due to the attendance of Bishop Eukissos at the Synod (Council) of Sardica in 343. At Rethymnon Museum there is a lead stamp (bulla) dating back to the end of the 6th or the beginning of the 7th century, which testifies to the existence of the Archdiocese.

There are not many data available concerning the Diocese of Selino. Although various sources refer to the Dioceses of Lissos and Gavge in the broader region, these stopped operating under the Arab occupation. In 1645 the Diocese of Kissamos started operating again with its See at Episcope. During the Venetian occupation, there were several monasteries in the region that tried and managed to preserve Christianity.

The best known among them is the Monastery of Chrysoscalitissa, which became a literary and education centre. Under Ottoman occupation the Diocese remained inert between 1831 and 1860, when it joined the Diocese of Kydonia. Similar to all Orthodox dioceses, the Diocese of Kissamos and Selino resisted the Ottomans. Indeed, Bishop Melchizedek and Deacon Kallinikos were hanged.

In 1962 it was promoted to a Metropolis. The current Metropolitan has been Mr. Amphilochios, as of 2005, with 80 parishes, 8 monasteries and 64 priests in his jurisdiction.