During the Byzantine times, a number of Early Christian basilicas were erected on Patmos and among these was a Grand Royal Basilica in honor of Saint John, built c. 300-350 at the location where the Monastery of Saint John the Theologian stands today.
Early Christian life on Patmos barely survived Muslim raids from the 7th to the 9th century and during this period, the Grand Basilica of Saint John was destroyed.
In 1085, though, a zealous Byzantine monk, the Reverend Father Christodoulos was forced by the Turks to abandon his temple in Asia Minor and went to the island of Kos were he founded a monastery. There, he met the monk Arsenios Skinouris who asked him his help to build the Monastery of Saint John in Patmos, only a 5 min. drive away from Patmos Villa Sophia.
The construction of the monastery started in 1101, after the permission of the Byzantine Emperor Alexios Komninos the 1st, who gave to Christodoulos the complete authority over the island of Patmos. As a result, the Monastery’s power was to extend over the island’s borders, to such a degree that the island was never occupied by neither Turks nor Venetians and the only attacks came from pirates there and then.

The fame of the monastery grew, a settlement started to expand around it and during the end of the 12th century, the island of Patmos was transformed into a large commercial center.
In 1207, the Venetians conquered Patmos and the reign was given to the Duke of Naxos. Supported by him, the island became a semi-autonomous monastic state and gained great wealth and influence.
In 1340, the Knights of Saint John who had seized Rhodes conquered the island of Patmos and, in the following centuries, population was expanded by infusions of Byzantine immigrants fleeing the Fall of Constantinople in 1453, and Cretan immigrants escaping the fall of Candia in 1669.