Amorgos was originally inhabited by seafarers from the Asia Minor coast around the 4th millenium B.C. Numerous grave sites (Tholi) and many Cycladic figures attest to the early, middle and late Cycladic periods which the island went through. The largest Cycladic figure, approximately one-meter tall , was found on Amorgos and can be seen on display in the Archaelogical Museum in Athens. The Cycladic period was very prosperous for the island since it was the nearest Cycladic metal center off the Eastern coast. Amorgos has had numerous names throughout its history. It has been called Pagali, Karkisia and Psychia. Its present name drives from the Mourgos plant from which a rare red dye was extracted to colour royal tunics. As numerous as its names are the number of invaders. Amorgos was colonized by Assyrians, Mylesians, Naxians, Samians and Cretans. It was a member of the Delian league during the Hellenistic period when it was under the Athenian control. It consequently passed to the Macedonians, Ptolomes and then to the Romans who used it as a place of exile.

The island passed to Venetian rule in the beginning of the 13th century . The Turkish admiral Barbaric conquered the island for the Ottoman Empire in the beginning of the 16th century. Amorgos gained its independence in 1823 and the monastery in Chora founded the first Lyceum in free Greece.