According to Greek Mythology the island took its name from the hero Mykonos and that on Mykonos, Hercules killed the Giants and the large rocks still found on the island are their pertified bodies.

There were two ancient towns on the island. The Ionians arrived from Athens in the 9th century BC. In general terms, from that time on Mykonos shared the same fate as the rest of the Cyclades. In the beginning it was under Athenian rule. But it played second fiddle to neighboring Delos which was a religious "holy/sacred place of Apollo" center for many centuries.

The Venetians conquered the island in 1207 and the Turks in 1537. It played a noteworthy role in the Greek War of Independence of 1821. The people of Mykonos gave their boats to Admiral Tombazis and when the Turks tried to invade the island in retaliation the islanders, led by the heroine of Mykonos Manto Mavroyenous, successfully repulsed them.