According to archaeological findings, Koufonisia were inhabited since Prehistoric Times.
Excavations in region Epano Mili brought into light important findings from the first periods of Cycladic Civilization. One of the most important findings from this period is a fryer shape vessel, exhibited in Naxos’ museum.
Excavations in the east shore brought into light findings from the Hellenistic and Roman times.
In the course of history Koufonisia followed the fate of Cyclades islands. They met the domination of Venetian and Turkish, who, mostly in the 17^th century, run against each other for the governance of Aegean Sea.
Koufonisia set free along with the rest of Cyclades islands and incorporated with the young Greek nation in 1830.