Thira was closely related to Minoan Crete and develped a significant civilisation similar to that of Minoans. However, around 1500 B.C., a terrible volcanic erruption blew up the central part of the island and caused the disruption of island's civilisation. Today a minoan city has come to light and is one of the most important historical sites in Greece. It is called the "Aegean Pompei"

In 11th century the island was inhabited by Dorians from Sparta and in 7th c. B.C. the islanders founded the colony of Cyrini in North Africa. During the following years, Thira was conquered by Persians, Athenians, Macedonians, Ptolemeos kings of Egypt and finally by Romans.

During byzantine period the island suffered by Saracene raids. Today one can see the church of Episkopi, which was built by Emperor Alexius First Comnenus in 11th century and the frescoes are still in good condition. After 1204, the crusader Marco Sanudo conquered Santorini (Santa Irini), as the Venetians renamed Thira. Later the Varotsi family ruled the island until 1538, when the moslem pirate Barbarossa conquered Santorini, on behalf of the sultan. Later sultan Suleiman granted Santorini to the Jewish Joseph Nazi. Santorini like Tinos, Siros and Naxos had catholic populations and did not participate in the Greek Revolution of 1821. Catholics were protected by Vatican and were not harassed by the ottoman tyrants. Santorini or Thira became part of Greek state in 1830, after 600 years of foreign occupaion.