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Human settlement has come and gone in these is lands, and our knowledge of their history is consequently patchy. Until the first excavations in the late 19th century, there was no awareness of the extraordinary human activity amongst these islands in the 3rd millennium bc, and its importance for sub sequent history. Some of the earliest lessons in the handling and shaping of marble and the managing of sea-vessels must have been learnt in these islands and their waters. It has even been suggested that the island of Keros was a central, sacred island—a sort of proto-Delos —for the area in the Early Bronze Age. The importance of these small Cycladic centres later diminishes in a new world-order, polarised in the Middle and Late Bronze Age between the cultural and commercial powerhouses first of Crete, then of Mycenaean Greece. During the Geometric period two relatively short-lived settlements on Donousa and Kato Koufonisi flourished. And then the lights virtually seem to go out. Keros, Ancient Keria, figured in Athenian tribute lists in 425 bc. Otherwise, little apart from the evidence of Hellenistic forts on Herakleia and Schinousa sheds light on these islands during the Classical and Hellenistic periods. The Romans had installations on them, but used them mostly as places of exile. A discreet Early Christian presence is evident on Schinousa, but the islands were too vulnerable to piracy and raiders for it to have had any continuity under Byzantine rule, which appears to have largely ignored the area. The archipelago became itself a base for pirates preying on the fertile shipping routes through the area. In the 18th century Schinousa and Herakleia belonged to the Chozoviotissa Monastery on Amorgos, which evidently derived supplies of timber from the former; the other islands were used as seasonal pasture by the inhabitants of Amorgos, except for Donousa which had a permanent population and paid a yearly tithe to the Sublime Porte during the period of Ottoman dominion.
In 1832 the islands were incorporated into the Greek State together with Naxos . Donousa had a growing population at the end of the 19th and in the early 20th century working the iron-ore mines on the island, which closed in 1938 at the outbreak of war. In 1941 the islands were occupied by the Italians and finally liberated from subsequent German occupation in 1944. Electricity was only brought to the archipelago in the mid 1980s.
Koufonisia Island is part of the Lesser Cyclades group