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.
The church of St. John Baptist is located in the center of Margarites and is a single – aisled vaulted church. Below the plaster, frescoes of 1383 have been revealed.
The Church of St. John the Theologian in Margarites is located at the southwest side of the village. It is a single-room vaulted temple and its interior bears traces of frescoes and an impressive stone iconostasis (icon shrine). On each side of the temple there are three blind arches.
The double church of the Transfiguration of Christ and Saint Anne is located in the cemetery of the village Ancient Eleftherna. The original church of the 10th century bears frescoes of the 12th century, has a dome and was built on the ruins of an older temple of the 6th century.
The church of Agios Dimitrios is a very special four aisled Byzantine basilica with a dome in the fourth aisle. A nave survives with a frescoes of St. Demetrius. It is considered to have served as the Diocese of Ario and was built at the site of an ancient temple of goddess Artemis (Diana).
300m away from the monastery of Halepa there is the church of Agia Marina with old frescoes. The church bears the coat of arms of the family Kallergis, one of the most important families of the Venetian period, implying that the region was one of their fiefdoms.
The Cathedral of Saint John is located at Episkopi, province Mylopotamos, and is a cruciform temple with a dome. It was built in the 13th century on the ruins of an early Christian basilica of the 5th century. It became the cathedral and the seat of the Diocese of Avlopotamos during the Venetian Era. Inside, on the surving dome we meet some frescoes of the 14th century following the Palaeologean style.
One of the most interesting religious monuments is found just north of the village Damavolou in Mylopotamos province. It is the church of Saints Constantine and Helen, which is built with the same architecture Cretans used to build the vaulted tombs and the mitata. The church is quite new, but it is worth mentioning due to its exceptional architecture.
The basilica was excavated in 1948 by K. Kalokyris and N. Platon, and was built in the 5th-6th century, like most seaside basilicas of that era. It was violently destroyed by Arab invasion in the 7th century, but continued to be used till the 9th century.