The province of Milopotamos hosted many small monasteries and hermitages. The rugged coastline hosted many ascetic centers, which were later moved to the innerland due to the threat of the pirate raids.
At position Katsivelos in Ancient Eleftherna the archaeologists have revealed the ruins of an imposing basilica. The basilica was built on the site of an older temple of the 3rd century BC, probably dedicated to Hermes and Aphrodite. The basilica was founded by the Bishop of Eleftherna Efratas around 450AD and was dedicated to the Archangel Michael.
The village Skepasti takes its name after the Byzantine church of Panagia Skepasti. There is legend about the Church worth mentioning. Once, pirates landed in the area and captured many girls, which were later sold as slaves to a Turk from Izmir. Among them was the wife of the priest of Skepasti.
The church saves two layers of frescoes. The oldest layer is located in the west corner dates back to the 11th century. The frescoes of the south part of the corss dates back to 1323.
One of the many churches that are devoted to Saint John, but remains unknown is located on the road connecting the villages Episkopi and Kefali. Agios Ioannis (Saint John) stands right on the edge of the road and at first glance seems to have the appearance of a modern church.
Inside Margaritsano gorge we meet the Byzantine church of Agia Paraskevi, which can be accessed Pigouniana via a dirt track. This is a small single-nave barrel-vaulted temple with its interior adorned by frescoes of the Venetian era.
In the center of the small village Erfi in Mylopotamos province we meet the church of Saint John. The temple bears frescoes in good condition, dating back from the 14th century.
The imposing church of Agios Georgios in Kalamas, province Mylopotamos, dates back to the 12th century and is one of the most impressive churches in the prefecture of Rethymnon. It has a special architecture, as it is cross-shaped with two narthexes in front and a dome at the center of the cross, reminding of a three-aisled church.
Near the primary school of the village Skouloufia there is the ruined church of Panagia (Virgin Mary). The roof of the temple has collapsed and the church dates back from 1410. There are no frescoes surviving, but a very beautiful window survives.