Patmos is inhabited since 3000 BC, but the identity of its first inhabitants is still unknown. Finds have excavated various buildings, cemeteries, fortresses, and evidence of an ancient acropolis, testifying the existence of a densely populated area in the past.

Patmos declined when the Romans conquered it. It was used as a place of exile for convicts. This is how Apostle John came to Patmos. He conveyed the inhabitants to Christianity and wrote the Book of Revelation, the Apocalypse. Patmos then became a place of worshipping and pilgrimage and actually.

During the Byzantine times, the inhabitants of Patmos built a Grand Royal Basilica in honor of Saint John. During the Arab raids from the 6th to the 9th century the basilica was destroyed. In 1101 the construction of the Monastery of Saint John the Theologian started. The fame of the monastery grew and a settlement started to expend around it. During the end of the 12th century, the island of Patmos was transformed into a large commercial center.

In 1522, the Turks came to the island; after a while, they left the island, which they just forced to pay some taxes. When the Turkish-Venetian Wars ended, tranquillity returned to Patmos and the island flourished, becoming once again an important commercial center. Massive fortifications were built around the monastery as a protection from the pirates. In 1655, Patmos was governed by the monks and prospered again. Its growth stopped in 1659, when the Venetians, conquered and destroyed the island of Patmos. With shipping, commerce and the efforts of the inhabitants, Patmos regained its lost nobility, glamour and prosperity.

The Russians conquered the island in 1770, after the Turkish-Venetian War. The Greek Revolution started in 1821 and managed to gain the independence of Greece in 1832. The treaty signed in London did not include the islands of the Dodecanese as part of the newly built Greek State and therefore fell again under Turkish occupation.

The Italians occupied all the islands of the Dodecanese in 1912, with of course Patmos, and remained there until 1943, when the Germans took over the island. In 1945, the Germans left and the island of Patmos remained autonomous until 1948 when it joined the rest of independent Greece with the rest of the Dodecanese Islands.

In 1981, Greece declared Patmos a “Sacred Island'', and in 1999 UNESCO included The Historic Centre (Chora) with the Monastery of Saint John the Theologian and the Cave of the Apocalypse in its World Heritage Site List. Patmos is also part of the COESIMA network, as one of the seven most important pilgrimage sites in Europe.