Inhabited since prehistoric times, Koufonissia were centers of the Cycladic Civilization – as proven by the archaeological finds in the Epano Myli area of Ano Koufonissi.
A frying pan-shaped vessel, with a nine point star carved on it, is considered the most important of these finds- kept at the Naxos Archaeological Museum.
Two Protocycladic settlements have been found on Ano Koufonissi, the first on the eastern side of the present-day village and the second near the chapel of Agios Nikolaos, at Potamia position. The only excavation that has been carried out at Kato Koufonissi is at a position of the later Cycladic period.
Nevertheless, finds on the ground surface prove the existence of Protocycladic housing and burial installations at Panagia and Nero – at the northern and southern parts of the isle respectively.
The ancient names of Koufonissia are not known with certainty, even though they are referred to as “Fakkoussae Islands” in the Corpus of Inscriptions.
The sea area between Ano and Kato Koufonissi was known as Kofos Limin (Deaf Harbor) – a name that defines a location that is sheltered and secure.
Apart from two Roman burial inscriptions, kept today at the Archaeological Collection of Chora, Amorgos, there are no written sources referring to the inhabitation of the isles in historical times.
Nevertheless, broken fragments of Roman vessels have been found and housing remains are still visible at Loutra position, next to the sea. The finds on presently uninhabited Keros, the isle opposite Koufonissia, are significant.
In antiquity it was called Keria and the first reference to this name dates to 425 BC, on an inscription of the taxpaying allies of the Athenian Republic. According to the inscription, the isle was inhabited during Classical antiquity. During the Middle Ages until the establishment of the new Greek state it was used as a base for pirates.
The oldest known archaeological reference is that of U. Kohler (1884), who attributes to a tomb on the island (but without determining the precise location) the two famous figurines kept at the National Archaeological Museum in Athens, of the harpist and of the flute player, together with two female figurines of the common type with folded arms – which we now know to belong to the Protocycladic II period.
One more harpist’s figurine, at the Metropolitan Museum of New York today, is thought to originate in Keros, while the large head of another figurine is exhibited at the Louvre, Paris.
The rest of the history of Koufonissia is in common with that of the rest of the Cyclades. They came under the occupation of the Venetians and the Turks who clashed several times, mainly in the 17th century, for control of the Aegean islands.
The inhabitants, sometimes out of need and other times out of option, often collaborated with Maniots (from the Peloponnesian district of Mani) or other pirates who used the strait between Ano and Kato Koufonissi as a safe haven. The two isles were liberated and incorporated into the modern Greek state with the rest of the Cyclades in 1830.