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The name Kalloni (Beauty) appeared after 1928. Till then the village was known as Skilloi, an ancient name after the plant skilla maritima or skillokrommyda (Drimia maritima, sea onion) that thrived in the territory. This region must have been inhabited since Minoan times, as ruins of a Minoan settlement have been found along with ceramic fragments (ostraka) and archaic figurines at Fanari location. At the same location there is a Byzantine rural chapel dedicated to St. Fanourios, probably an old monastery; residents have renovated it and they hold a major feast there on 27 August.

In the centre of the village there is an old fountain bearing the Byzantine double-headed eagle, and an Ottoman inscription mentioning the name of the man who renovated it.

At Ammoudara location, there is the old Agia Fotini church, rumoured to have been built by Nikephoros Phokas when he liberated Crete, where there is an important Byzantine mural. This must have housed a convent deserted before 1600 A.D.

The patron saints of the village are St. Nicholas and St. Ambrose to whom a two-martyr church is dedicated. There is also the church of the Annunciation (Evangelismos) and Agiou Antoniou (St. Anthony) church, as well as the renovated church of Kera-Kardiotissa (Lady of Karydaki), which is the cemetery church.

Kalloni was the birthplace of Gerasimos II, Palladas, the Patriarch of Alexandria, famous for his wisdom and piety.