The history of Amorgos begins many centuries before e, as evidence indicates that the island has been inhabited since the Prehistoric Era.
Excavations have revealed that organized life existed in Amorgos from the 4th millennium BC, at the end of the Neolithic age. During the 3rd millennium BC, Amorgos participated in the development of the Cycladic civilization: settlements and cemeteries have been discovered as well as twelve citadels. The large number of small works of art (ceramics, metalwork, marble idols) found on the island show the cultural advance of the people and indicate that they were in frequent contact with the other Cycladic islands as well as Crete. At the end of the Cycladic period, the Cycladic civilization in Amorgos lost its vigor due to the growth of the Cretan superiority in the Aegean. From this time, Amorgos became an important sea trade station for the Cretans who controlled and colonized it.
During the Archaic period (7th-6th century BC), Amorgos was colonized by cities of Ionia, which gave the island a fast political and social development. During the Classical era (5th-4th century BC), the three cities of Amorgos (Arkesini, Aegialis and Minoa) functioned as a federation, manufacturing, trading, and shipping. Its inhabitants took part in the Persian Wars, especially in the Battle of Salamis in 480 BC, in which the island used one of its ships. In 478 BC, Amorgos joined the Athenian Alliance. After that, like all the other Cyclades, it lost its autonomy and paid a yearly tax to the Athenian state.
In 337 BC, the Macedonians dominated the Hellenic affairs: Amorgos became part of their state. The disputes of Alexander the Great's successors brought Amorgos under the influence of the Hellenistic State of Egypt, the Ptolemies. After the 2nd century BC, the Romans took control of Amorgos.
It was only with the decline of the Roman Empire that the three ancient cities of Amorgos lost their strength and were destroyed causing decay to several monuments, such as the Hellenistic tower in Arkesini. It was in those years that Christianity was established in Amorgos and early Christian churches made their appearance. During the Byzantine Period, the village of Chora was formed, in the mountainous center of Amorgos, to be protected from piratic invasions. In the 11th century, the famous Monastery of Panagia Hozoviotissa was founded by the Byzantine Emperor Alexios Komninos.
The year 1207 was important for the history of Amorgos and all Cyclades. The Gizi Venetian family took control of Amorgos but they were quite powerless to protect the island so, during the next two centuries, it became a permanent pirate shelter. In desperation, a lot of people left their homes and went to safer places like Crete. Between 1200 AD and 1579 AD, the island was occupied by the Byzantines and the Venetians, and then, from 1579 AD to 1821 AD, Amorgos was occupied by the Ottomans. At that time, the island became a small self-governed democracy called Amorgos Community, taxed by the Sultan.
After the end of the Greek Revolution, Amorgos and all the Cyclades islands became part of the Greek State.
In 1835, the municipality of Amorgos was formed, the easternmost boundary of the New Greek State, and had one of the first schools to function in free Greece (organized under the initiative of the Hozoviotissa Monastery).
From Roman times until the 20th century, Amorgos was a place of exile. In fact, during the period of the Greek junta (1967-1974), many democrats who opposed the regime were exiled to the island, including one of the now most powerful men in Greece, the businessman and philanthropist Vardis Vardinogiannis.