Archaeologists accept that the Cyclades were inhabited in the Mesolithic as obsidian from Milos has been found in Franchthi Cave in the Argolid in contexts dating from 11,000 BC. This means that there was interaction between the islands and mainland Greece in the Post-Pleistocene.
However, the first definite settlement evidence from the Islands comes from the early Neolithic, in the 5th millennium BC. It is believed that only farming societies were able to exploit and populate the islands effectively, due to the limited resources available for hunter-gatherers. The Grotta site at the Chora of Naxos has produced Late Neolithic material and shown continuous settlement into the Chalcolithic and Bronze Age. Based upon its size and situation Naxos became one of the most influential centres of Cycladic culture from 3rd millennium BC, with the site at Grotta continuing as Naxos main settlement into Mycenaean and Geometric periods.
In the early archaic period Naxos founded a colony on Sicily and another on Amorgos, and had a developed a successful economy based on its marble quarries and sculpture. In the 6th century BC the Tyrant Lygdamis took control of Naxos. The Island was unsuccessfully besieged by the Milesian Aristagoras, who to save his own position started the Ionian Revolt against Persia in 499 BC. When that too failed Persia retook much of the Aegean and Naxos lost the dominant position that she once held. Naxos then came under Athenian control, and briefly Sparta, in the 4th century BC, before passing to Macedonian, Ptolemaic and later Roman rule. Naxos like most of the Aegean had fallen into a pattern of being a possession of the larger powers and being governed from elsewhere. Naxos does not have a natural harbour and did not develop political power and ambitions of her own in this period. However, her size, productivity and population made Naxos an asset from which to dominate the Cyclades.
Under Byzantine rule Naxos flourished, again her size and agrarian output gave the island an economic advantage. The island was placed administratively under Rhodes. Arab expansion in the Mediterranean saw the abandonment of Chora as town and political centre and a flight from the coast to the inland. Kastro Apalirou in the centre of the southern part of Naxos was constructed probably sometime during the 7th century AD as a fortified urban citadel and refuge. Halki in the main agricultural district was also developed as a political centre at this time and an archbishopric was established here at least from 1083. This situation of dual political centre and inland rule continued for at least 500 years until 1207, when Naxos came under Venetian rule. The threat from pirates and raiding in the Mediterranean ceased and, trade increased in importance. The newly established Duchy of the Archipelago moved the capital back to Chora, and Naxos moved into a period of stability and economic growth.