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Koufonisi has been continuously inhabited since the Prehistoric period. It has been a centre of early Cycladic culture, as presented by the archaeological discoveries in the area of Epano Miloi, with most important, a pan shaped vessel with a nine ray star engraved on it, which is today kept in the Museum of Naxos.

In various periods of their history the islands were pirate bases, with whom residents collaborated several times, probably because they did not have any other choice.

The islands were relieved of the Turkish rule after the revolution of 1821, and were linked with Greece along with the rest of the Cyclades.
koufonisi map