Excavations have revealed that organised life existed in Amorgos Greece from the 4th millennium BC, at the end of the Neolithic age. During the 3rd millennium BC, Amorgos island participated in the development of the Cycladic civilisation: settlements and cemeteries have been discovered as well as twelve citadels. The big quantity 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 civilisation in Amorgos lost its vigour 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 colonised it.
During the Archaic period (7th-6th century BC), Amorgos is colonised by cities of Ionia, which gave to the island a fast political and social development. During the Classical era (5th-4th century BC), the tree cities of Amorgos functioned as a federation, manufacturing, trading and shipping. Amorgos took part in the Persian Wars, especially in the Battle of Salamana 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 they 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 Chora was formed, in the mountainous centre 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 AC and 1579 AC, the islands saw the occupation by the Byzantines and the Venetians. From 1579 to 1821 AD, Amorgos was occupied by the Ottomans. That time, the island became a small self-governed democracy called Amorgos Community, taxed by the Sultan.
Just before the Greek Revolution, many inhabitants of Amorgos (Georgos Exarhopoulos, Antonis Gavalas and more) had become members of the Society of Friends, a secret society who was preparing the ground for the Greek Revolution. After the end of the 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 (organised under the initiative of the Hozoviotissa Monastery).