The islands have been inhabited since the Prehistoric Age. Excavations in the Upper Myloi area have revealed significant burial findings of the early Cycladic Civilization period. One of the most significant findings, a pan shaped vessel with an engraved nine- rayed star, is exhibited in the museum of Naxos.
Another excavation site, in the south end of the East Coast, has brought to light findings from the Hellenistic and Roman times.
In the course of the centuries, Koufonisia, like all the Cycladic islands, went under the rule of the Venetians and the Turks, who, during the 17th century, fought to gain control of the Aegean Sea islands. The Koufonisians often co-operated with the pirates, who used the straight separating the two islands as safe refuge.
Koufonisia were liberated together with the rest of the Cyclades islands in the Greek War of Independence (1821-1829). They became part of the newly founded Greek State in 1830.
Keros (The Mystic Island)
Ancient Kereia or Keria, is mentioned for the first time on an inscription in 425 B.C. It is a rocky small island, 1.5 nautical miles southeast of Koufonisi, and has been a significant center of Cycladic Civilization (3000 - 2000 BC). Two of the many significant findings, are the famous marble statuettes of the harpist and the flutist, displayed at the Archaeological Museum of Athens. Many believe that Keros is identified with «Asteria», the island where the ancient Greek Gods of mythology Apollo and Artemis were born - and not on Delos as is generally believed. The supporters of this theory find traces of Homer, the Orphics and other ancient sources that seem to be persuasive. Keros is also the home of a well kept secret which archaeologists have been trying to reveal for years. Excavations, probably around 1958, brought to light 350 statuettes, all fragmented with the exception of 12, and a number of marble vessels and earthen pots. All these findings have since been called the "treasure of Keros". How, why, and for what purpose, this great number of purposefully fragmented statuettes was found in Keros, has puzzled archaeologists for years.
However, excavations during the summer of 2006 support the belief that Kavos, the exact place where the statuettes were found, was a 4,500 year old ceremonial center, the oldest ritual site in Greece. Up to then, archaeologist could not be sure whether fragments of the statuettes had been smashed in antiquity or in more recent times by smugglers. But the recent excavation on an undisturbed patch dating back to 2,500 B.C., revealed material which was already broken in fragments before it became buried. Furthermore, "the rarity of joining pieces made it clear that they were broken elsewhere and were brought already in fragmentary form" said an announcement by the Greek and British archaeological team heading the excavations. The materials came from Naxos, Amorgos, Syros, and mainland Greece, making Daskalio Kavos "the first major ritual centre of Aegean prehistory". Excavations continue.