According to the archaeologists, the unfortified ancient city of Thera was founded in the 8th century BC by Dorians from Laconia and probably of Boeotia on the hill of Mesa Vouno. The town also survived through the Hellenistic period (3rd-2nd century BC). Thera still remained robust since, as testified by Herodotus, King Grinosin the mid-7th century BC organized the colonization of Cyrene, in Libya, by the population of Thera. This city flourished and it was the place of origin of the poet Callimachos.
Apollo Karneios, Asclepius, Hermes, Heracles and Dionysus were worshiped on the island. The temple of Apollo Karneios, the heroon of Thera, the ancient theatre, the Ephebeum and the sanctuaries of Isis, Anubis the Serapis which are related to the period of the Ptolemies of Egypt were found during the excavations of 1898 by Hiller von Gaertringen.
Although the island was considered to be Doric during historic times, however inscriptions show that also Ionians lived there. During the Persian wars, Thera “sided with the Medes” as the residents offered “land and water” to Xerxes. As Milos, Anafi and Folegandros, Santorini did not participate in the Delian League. In 425 BC at the beginning of the Peloponnesian War, Thera submitted to the naval power of Athens and paid atax of three talents which later increased to five.
During the Hellenistic period, Thera developed as a naval base by the Ptolemies of Egypt. During the time of the Roman conquest it was part ofthe «Province of the Islands» (Provincia Insularum). Coins of the island that were cut from the time of Marcus Aurelius to the time of the emperor Commodus with the inscription “Thereo” or “Thereon” were found. During the Byzantine period, administratively, it belonged to the Province of the Islands which had Rhodes as its capital. After Justinian’s era, Thera together with Therasia became part of the Theme of the Aegean Sea which had Samos as its capital. Christianity appeared on the island as early as the 4th century. The construction of the church of Panagia Episkopi in Mesa Gonia is associated with the time of Alexios I Komnenos (1081-1118).
The division of the territories of the Byzantine Empire in 1204 after the Fourth Crusade was associated with the foundation of the Duchy of the Aegean in 1207 by Marco Sanudo. He gave Thera and Therasia to Jacob Varotsi. In 1269 the island was occupied again by the Byzantines, but during the seven-year war of Andronicus II Palaeologus with the Venetians it returned to the house of Varotsi. In 1318 Santorini became the target of the destructive attack of the Giustiniani of Chios. In 1335 Nicholas Sanudo drove the Varotsis away permanently and annexed the island to the Duchy of Naxos. After 80 years, John Jacopo Crispo ceded it to his brother Niccolo Crispo, while he ceded Therasia to his brother Mark who was the feudal lord of Ios. According to historical sources, in the mid 15th century Thera had experienced great disaster from pirate raids and its population had decreased to the number of 300 residents. For this reason, Santorini actually paid the Duke of Naxos only 500 ducats.
Jacopo III Crispo in 1480 ceded the island as a dowry to Dominic Pisani who had married his daughter Fiorentsa. The Pisani descended from a noble generation of Venice and was the son of the Duke of Crete. After the death of Jacopo III, his successor, John III Crispo, had a dispute with Pisani who claimed the dominion in the Duchy of Naxos, he captured the castle of Skaros (La Roka) and he annexed the island. In 1492, after his death, Venice captured it and ceded it back to the Duchy of Naxos.
During the Rule of Franks, Thera became the seat of the Roman Catholic bishop. At this time it appears that the name Santorini was given to the island, from the church of Agia Irini (Santa Irene). Many of the residents became Roman Catholics
In 1537, the legendary pirate and later admiral of the Ottoman fleet, Hayreddin Barbarossa, who came from Mytilene, captured and looted the island.
The Turks until 1579 ceded Santorini to the Jew Joseph Nasi who would in change pay them a tax. At the request of the inhabitants of the Cyclades, the Sultan Murad III (1574 - 1595) gave to Santorini as well after his ordinance major commercial and self-administration privileges. Within this framework, the island showed growth in agriculture and its main export product became the famous wine of Santorini. In 1770, the island's population reached 9000 residents, while from the late 18th century the island had an important naval fleet that enabled it to maintain commercial relations with the major ports of Alexandria and Constantinople.
On the 5th May 1821, on the day of the celebration of the patron saint of the island Saint Irene, the delegate of Demetrios Ypsilantis, Vangelis Mazarakis raised the flag of the Revolution. During the early years of the Modern Greek state, Santorini presented considerable commercial traffic. The big ships of the island transferred wine to Russia and from there they brought wheat to the island and to the ports of France, Italy and England. Also, exportation of Theran land to Austria and to Greek ports took place. Shipowners had ships of great capacity. In 1852, 7222 people lived in Thera and it had a merchant fleet of 200 ships of a capacity of 14,755 tons, 31 of which exceeded 200 tons.
A very important fact in the recent history of Santorini was the devastating earthquake of 1956, which led many residents of Thyra to internal migration. But they returned a few years later and started to rebuild the villages of the Caldera, which are now, thanks to their cave buildings, jewels of the Aegean and a pole of attraction for visitors from all over the world.