Rule of the West
In 1207 Marcos Sanudos founded the Duchy of Archipelagos (or Naxo's), so Thera and Therassia were ceded to Iakovos Barotsi and were owned by his family with short intervals until 1335. During the Venetian era the feudal system applied and Santorini became the headquarters of the Catholic Archiodese, one of four in the Duchy. In 1335 Nicolo Sanudo expelled the Barotsi family and added the island to the Duchy of Naxos.
After 1487, it was Venice that set the fate of the islands in the Duchy of the Aegean (1487). During the rule of the West, the islands suffered a great deal of pirate invasions from the Franks, the Muslims even the Greeks, which forced residents to live in fortified settlements called Kastelia.
To make matters worst the competition among the local Latin dynasties and between the Duke and the Sultan, increased. At the same time, the coexistence of the two Christian communities, Catholic and Orthodox, often caused tension instigated by the religious leaderships of both communities.
In 1537, Khayr ad-Dīn Barbarossa, the notorious ex pirate and admiral of the Turkish fleet, took over the island in the name of the Sultan. In 1566 it was ceded to Joseph Naji, a wealthy Jewish banker who governed the islands through a representative until 1579. Then Santorini and the other islands, except Tinos, were finally ceded to the Ottoman empire.
* Source: "Santorini: And the sea brought forth the earth"/ Topio Publications/ From the text of archeologist Kiki Birtacha.
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