The monastery of St. John was founded in 1088 by the monk Christódoulos, with permission of the Byzantine emperor Alexios I Comnenus. It was build near the cave where it is said, the apostle John, who was banned by the emporer Domitianus, wrote the last book of the New Testament, the Apocalyps (or revelations of John), in 95 AD. John was send to Patmos because he had spread the word of Christ in Ephese, but after Domitianus died in 97 AD he supposedly returned to Ephese and died there at a very old age. The Cave of the Apocalyps is now a part of the small monastery complex, just under the top of the mountain where the Chora is situated. The cave is still in fairly authentic state and can be viewed.

The monastery gives the impression of being a fortres that offered protection from pirates. The monastery church is richly decorated with frescoes from the thirteenth century, the library with old books, writings and documents, and the treasure chamber with an abundance of relics, icons and other valuable items. The attractive village (Chora) at the bottom of the monastery developped because workmen and artists, that helped build the monastery, started to live here in order te be protected from the never ending threath of pirates.