Long before the hot springs acquired a reputation, people were living on Kythnos. At Maroulas on the northeastern coast, close to Loutra, archaeologists have identified a Mesolithic settlement dating from approximately 10000 to 8000 BCE — one of the oldest known habitations in the Cycladic islands. Excavations in 1996 uncovered intact human skeletons, stone artifacts, and part of a floor pavement, suggesting a long-term community of hunter-gatherers who had established themselves on the Aegean shore during the Stone Age. Large portions of the site have since eroded into the sea. Further back in time, Bronze Age findings near the summit of Mount Profitis Elias indicate that Kythnos was supplying raw copper to other Aegean islands during the third millennium BCE. The island's ore-rich geology runs deep: copper in prehistory, iron in the 19th and 20th centuries, the same rock serving human purposes across five millennia.

Medieval Kythnos changed hands repeatedly. In 1207, the Frankish lord Marco Sanudo incorporated it into his Duchy of the Archipelago. The Venetian Gozzadini family held it for generations thereafter. The Ottomans finally ended that era in 1617, taking the island's hilltop fortress — the nearly impregnable Kastro of Oria, where three sides dropped 500 feet to the sea — through what a local legend, recorded by the traveler Theodore Bent in 1885, describes as a ruse: a woman heavy with child approached the gate in apparent distress, the watchman's daughter opened it out of compassion, and Ottoman soldiers hidden nearby poured through. Whether true or apocryphal, the story lodged itself in the island's memory. The Kastro's walls still stand in the extreme northern headland, delineating the foundations of hundreds of long-vanished houses.

Kythnos has more churches and chapels than most places its size. The island counts well over a hundred of them, scattered across its 100 square kilometers of hillside, coastline, and valley. The two main villages express different characters: Chora, the island capital, has the flat-roofed whitewash typical of the Cyclades, with a large Greek Orthodox church at its center; Dryopida, a few kilometers south, has tiled, pitched rooftops that give it an almost mainland look, and its own dense cluster of religious buildings, including the Byzantine-classified churches of Saint Minas and Saint Savvas. The annual cycle of saints' days — each church has its own — structures the island's social year as it has for centuries, with outdoor festivals accompanying the liturgical celebrations.

For much of the 20th century, Kythnos was economically marginal. The iron mines in Dryopida, worked from 1835 to around 1940, gave a generation of Kythnians a supplementary income, but the ore ran out and the population declined as young people left for Athens. The tourist boom that transformed the rest of the Cyclades largely bypassed the island until 1974, when the construction of a proper deep-water mole at the port of Merichas finally allowed ferryboats to dock reliably. What followed was quiet but real: a gradual recovery, vacation houses on remote coves, and — unexpectedly — a pioneering role in renewable energy. In 1982, Kythnos established what became Europe's first wind park. With solar water heaters on nearly every house and photovoltaic systems supplementing the grid, the island has been running energy experiments since before most of the world was paying attention.

Today the island sits comfortably between its past and a modest but genuine present. Chora (population around 560 at the 2011 census) and Dryopida (around 325) maintain their winding, stepped streets — too narrow for vehicles, designed for a pace of life measured in footsteps. More than 90 beaches ring the coastline, many still unreachable by road. The crescent isthmus of Kolona, where two beaches almost meet across a sliver of sand, is particular. In 2023, Kythnos opened its long-awaited Archaeological Museum in a restored schoolhouse in Chora, displaying finds from the ancient temple at Vryokastro — over 1,400 objects excavated from a 2,700-year-old sanctuary dedicated either to Hera or Aphrodite. And beneath Dryopida, Katafyki Cave — one of the largest in Greece — offers a different kind of encounter with the island's layered past.