Between 1200 and 1579 AD, the island of Thera was part of the Byzantine Empire and was administered by the Venetians, who were responsible for the construction of several important, mainly defensive buildings. A period of Turkish rule followed (1579 to 1821), associated with the development of trade and naval power. On the other hand, however, there was a growing desire for independence among the islanders, which was fulfilled in the Greek War of Independence.
In 1204, the island of Thera (like the other islands in the Aegean Sea) passed into the hands of a Venetian named Marco Sanudo and thus became part of the Duchy of Naxos (or the Duchy of the Aegean). An important ruler of the island was Giacomo Barozzi, the Venetian baron of Santorini and Thirasia, whose descendants ruled the island until 1480. The duchy was then annexed to Venice in 1487.
The Venetians gave the island a new name after their patron saint, Saint Irene ("Santa Irini"), and thus the island of Santorini was created. Several new buildings were built on the island afterwards in memory of Saint Irene, including the beautiful Basilica of Santa Irini (dating from 1477).
However, the period of Venetian rule was marked above all by constant battles with pirate gangs and, to a lesser extent, by rivalries between the local rulers. This tense atmosphere led to the creation of five fortified settlements (castellations), which stood in strategic locations and were equipped with gates and watchtowers. Although these castellations were severely damaged by the earthquake of 1956, their remains have survived to the present day and are now interesting landmarks on Santorini. These are Skaros Castle (in today's Imerovigli), Pyrgos Castle, Emporio Castle, Akrotiri Castle (Punta Castelli) and Agios Nikolaos Castle (or Apanomerias) in the town of Oia.
Over the years, the Venetian rulers managed to negotiate a number of treaties of recognition from the Ottoman Empire. However, even this did not stop the Turkish raids and in 1579 the island of Santorini was finally conquered by the Ottoman admiral Piyale Pasha. The Turks called the island "Dermetzik", which translates as "small mill" (probably because of Santorini's numerous mills). During the Russo-Turkish War (which took place in the second half of the 18th century), the island briefly came under Russian rule, but soon came back under the control of the Ottoman Turks.
Under Turkish rule, the island no longer had to deal with pirate attacks and even built up its own merchant marine fleet. Santorini thus successfully developed its trade relations with the major port cities of the eastern Mediterranean and managed to maintain its privileged position during the following century. For example, manor houses from this period can still be found on the island today, which are evidence of the high standard of living of the local population.
After the outbreak of the Greek War of Independence, which began in March 1821 on mainland Greece, the island of Santorini followed suit in May, although the local Catholic Church had reservations about the move. The Santorinian naval fleet was very strong and played a significant role in the Greek War of Independence. The island of Santorini finally became part of the independent Kingdom of Greece in 1832 (with the signing of the Treaty of Constantinople).
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