Folegandros is said to have taken its name from the son of the Minoan king of Crete. The first settlers, however, are said to have been the Carians from Asia Minor. Another theory often put forward is that the Phoenicians, who used Folegandros as a base in the Aegean/Mediterranean, and, having observed the dramatic cliffs and rocky soil called it "Phelegundari" which in their language meant 'stony land'.

Little has been written about Folegandros during the Byzantine period; until the mid 17th century it was "an exarchate of the Patriarchate of Constantinople".

After 1204 the Venetians were in power, they controlled many of the islands of the central Aegean. It was during this period that the 'Castro' in Chora was constructed in order to protect the local inhabitants from the frequent pirate raids.

In 1715 Tzanoum Hotza, the Kapoudan Pasha, attacked the island and sold the population into slavery; only a few people survived. They later returned to Folegandros and after some time they invited several families from the neighbouring island of Crete and the Peloponnese to come and settle in order to re-populate the island.

In 1770 Folegandros was conquered by the Russians for 4 years until the Ottomans regained it until the Greek revolution of 1821.

A characteristic of Folegandros is how often throughout its history it has been used as a place of exile; from Roman times up until 1970 when it was home to the banished anti-government left-wing dissidents but inspite of its chequered past, it has the ability to adapt and survive as the last few decades can attest to; it has seen its population grow after years of migration due to the development of tourism, however, despite this, the population has not undergone rapid social change neither has the island been spoiled by this tourism, nor has it lost its character or charm.

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