The first inhabitants were Dorians, and later the island was colonized by Ionians from Asia Minor who worshipped the goddess Artemis. In the year 95, St John the Evangelist, was exiled in Patmos, where he lived an ascetic life and wrote the Apocalypse in one Cave. At the entrance the church Aghia Anna was built.

In 1088, the Greek Emperor, Alexius I Comnenus, granted Patmos to Snt Christodoulos, who had built the magnificent, fortified Monastery of Snt John (Aghios Ioannes Theologos). The monastery protected Patmos from pirates. The 900 manuscripts, the 2000 rare volumes and the 13000 documents that its library contains, make it unique. In 1207, Marco Sanudo annexed Patmos to the Duchy of Naxos. After the conquest of Constantinople by the Turks, many refugees settled on the island.

In 1770, Patmos was conquered by Russians. In 1821, the islanders participated to the revolution. Emmanuel Xanthos, one of the founders of Philiki Etaeria was from Patmos. After 1830 Patmos remained under ottoman occupation. In 1912, it was conquered by Italians and in 1948 became part of the modern greek state.