The archaeologists confirm that on the northeast coast of Kythnos near Loutra (baths), there is the oldest human settlement in the Cyclades. This position dates back to the Late Mesolithic period (8500-6500 BC). Findings of the Early Cycladic period (3rd millennium BC) have been found in the location Skouries.
An inscription on the pedestal of the statue of Zeus at Olympia testifies the participation of Kythnos in 480 BC in the naval Battle of Salamis, with a galley and a pentikontoros. According once again to Herodotus, the ships Paros anchored in the waters of the island waiting for the outcome of the naval battle. At the time of the Peloponnesian war, Kythnos was on the side of the Athenians in the battle of Aegospotami between Athens and Sparta in 405 BC, which led to the overwhelming defeat of the Athenians. In this battle we have the recorded participation of sailors from the island who were among the crew of Conon. It seems that the close relations of Kythnos to Athens went on until the end of the 5th century BC. In the sanctuary of Demeter at Eleusis inscriptions had been found referring to an amount which the “Common of Kythnos” had been paying as well as the possession of a temple on the island of Kythnos which gave revenues.
According to Pliny, Kythnos was famous in antiquity for the fine cheese, the good taste of which was due to some herb growing there. In 378 BC, during the growth of the Macedonians, the island participated in the alliance against Sparta, a fact that caused the sharp comments of Demosthenes. However, in a lost work of Aristotle titled “Kythnion Politeia” there is a reference to the political situation of the island. Along with the rest of the Cyclades Kythnos in 324 BC, during the era of the successor of Alexander the Great, One-Eyed Antigonus, participated in the Common of the Islanders" which had its headquarters in Delos. After 288 BC Kythnos goes to the hands of the Ptolemies of Egypt.
During the Roman rule, it was a place of exile and it seems that the mineral springs in the bay of Loutra were being used. These springs in later years became the reason to name the island Thermia. In the early years of Christianity in the northeast part of the island the capital of those years was founded that now it is known by the name Castle of Katakefalou or of Oria. After the capture of the island by the Franks, the family Gozzadini, which from 1337 until 1617 was in power in the island, settled there. Kythnos suffered a lot of damages in 1537 during the campaign of Barbarossa in Cyclades.
During the reign of King Othon a tragic event went down in history as the “Kythniaka”. Those who revolted in Nafplio in January 1862 against King Othon were exiled here - but when in February, the officers Loetsakos, Moraitinis and Skarvelis went to the island to free the rebels, they were pursued by the Navy and had to resort to the bay of Agia Irini where after a fight they were killed by the forces of the king.