According to excavations, the first human presence on the island dates back to the Neolithic Period. Santorini hosted an important civilization around 3600 BC. Discoveries made near Akrotiri and the famous Red Beach show the existence of an ancient Minoan colony. The city was very similar to those found in the island of Crete, with many wall ornaments and pottery showing naturalistic landscapes of animals and humans of the same ancient Minoan style.

In Ancient times, Santorini Island was known as Stongili, which means round in Greek. Strongili was the victim of an enormous volcano eruption in 1,500 BC. The eruption was so huge that many consider it to be the main cause of the destruction of the great Minoan civilization on the island of Crete, situated 70 nautical miles away. The specialists believe that the explosion was so strong that it created gigantic waves that reached the shores of the surrounding islands and Crete. After the explosion, the center of Santorini sank, and the many earthquakes that followed destroyed a big part of the rest of the island.

According to history, Phoenicians settled on ancient Thera around 1,300 BC and stayed for five generations. Then, around 1100 BC, the island was occupied by the Lacedaemonian. Around 825 BC, the inhabitants of the island, then named Thera, were using the Phoenician alphabet. In the 7th and 6th centuries BC, Thera had commercial and trade relations with most of the islands and cities of Greece.
During the Hellenistic Period, Thera, because of its central position in the Aegean, became an important trade center and a important naval base. Between 1200 AC and 1579 AC, the island was under Byzantine rule and the church of Episkopi Gonia was founded.

In 1204 AC the island surrendered to the Venetian Marco Sanudo and become part of the Duke of the Aegean. The name of the island was given by the Venetians after Santa Irini, the name of a catholic church. During the Turkish rule (1579-1821) the island succeeded in trading development with the ports of Eastern Mediterranean. The period that followed was quite prosperous.

Due to the wars of the 20th century, Santorini`s economy declined and the inhabitants abandoned the island after the catastrophic earthquake in 1956. The tourist development in Santorini begun in the 1970s and today it is one of the best tourist destinations in the world.