The 1600 B.C. eruption changed the form of the island. We do not know if all the residents evacuated in time before the great catastrophe, where they moved, or when they returned. Occasional findings in the area of Monolithos suggest habitation from at least the 13th century B.C.

According to Herodotus, the island named Strogili (round) due to its shape, was renamed Kallisti due to its beauty (kalos in Greek). Phoenicians settled in Kallisti. They were led by Kadmos who was travelling to search for Evropi (Europa) kidnapped by Zeus who had been transformed in a bull.

The settlers occupied the island for eight generations. Later on Spartans and their leader Theras, son of Autesionas, came along. In the 10th century the island became colony of the Dorians.

Geometric times (10th -8th century B.C)

There is not much data from the geometric times. Some researchers claim that in the end of 9th or early 8th century B.C. the residents together with those of Milo's and Crete's were the first to adopt the Phoenician alphabet. The cemeteries discovered in the SE side of Sellada and the one discovered on the edge of Mesa Vouno were built during the geometric period. Cemeteries were used systematically until 7th century B.C. and in the graves possibly placed were ancient statues of Kouros, probably imported from Naxos.

Archaid Period (7th-6th CENTURY B.C.)

During this period the residents developed relations with nearby islands such as Crete, Milos, Paros and with important centers of that time, such as Athens, Corith, Rhodes and Ionian centers in the eastern coast of the Aegean Sea. In 630 B.C. Therans founded Kirini, a colony in the northern coast of Africa.

Data for this period exist from findings in the cemetery located NE in Sellada which had been used until the 4th century B.C. and from findings in the cemetery in Kamari. Therans farmed, fished and traded with their own products. In the 6th century Thera had its own currency with two dolphins as an emblem.

Classic-Hellenistic times

Relations with the important centers of that time continued and wine was one of the most exportable products. During the Peloponnesian war, Thera supported Sparta as it was a Dorian colony. During Hellenistic years it became a nautical military base of Great Alexander's Ptolemaic successors and the island was used as a station for the southern to northern Aegean Sea routes. Important for them was the location of ancient Thera and the bays of Kamari and Perissa.

Christian-Byzantine period

Findings for this period are few and suggest that the centre during these years was in the SE side of Thera. In the 4th century there was an organized church with a Bishop. The first one is said to be Dioskouros (324-344). Christian temples were founded in the place where ancient shrines or temples used to be such as the one of Pythian Apollo in ancient Thera.

In the Byzantine period, Thera belonged to the theme of the Aegean Sea, but had no major political or military importance. Due to Arab invasions that took place during the 9th century, the residents moved to the inland, to fortified and unseen from the sea places. This era is marked by decline and poverty.

In the second half of the 11th century when the pirates' bases of operations were destroyed and the Arabs were weakened, the byzantine church of Episkopi Gonia was founded by Alexius I Comnenus. In the late 12th century, the byzantine fleet lost power, so the islands of the Aegean Sea were once again hit by piracy.