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From scientific research and the excavations on the hill of Kastro in Pythagorio, it is safe to say that Samos was inhabited as early as the Neolithic era.
The first settlers of Samos were Hisieis from the promontory Hision of Asia Minor and Astipalaians. Kares, Leleges as well as Pelasgoi were the first inhabitants of Samos as in most of the island of the Aegean Sea.

With the end of the Trojan War Ionians under the leadership of Proklis and Temvrionas colonized Samos. Paphsanias makes references to another wave of settlers coming from Phliouda of Peloponnisos under the leadership of Ippasos, the mythical ancestor of the Samian philosopher Pythagoras.

The city of Samos, todays Pythagorio becomes one of the most important cities of Ionia along with Militos and Ephessos. Around 600 BC the Samian colonized Amorgos, Thrace, Cilicia and they had developed important trade relation with Egypt.
During the rule of Polikratis (538 or 532 - 522 BC) the development of commerce and artisan trades along with the built of a war fleet rendered Samos a sea power first of all Greek and Barbarian cities according to Herodotus.
Typical was the new type of ship Samaina, which combined the requirement for storage space with revolutionary elements of a fast sea vessel.


 
Herodotus wrote that he admired Samos for three amazing construction feats - marvels - that he visited during his visit to the island. These were:
  • Ephpalinos Tunnel a water reservoir with an underground tunnel of 1036 meters in length. It was part of an extensive water distribution system for the ancient city of Samos, which had a population of 150000 people and according to other historical sources 300000 inhabitants.
  • The "land within the sea", the ancient port of Pythagorio, which is considered the oldest manmade port in the world.
  • Heraion, the temple of Hera, the richest and biggest temple of all Greek temples.
From the preclassical era we can also study and admire, finds from the palace of Polyctates and the ancient city of Samos, the ancient walls etc.

The economic development brought the development of science and art. World-renowned personalities of science and art who originated from Samos were:

  • The philosopher, mathematician and musician Pythagoras (580-500 BC). A personality with many interests, who combined mathematically the cosmological beliefs of Orpheus and gave functions and qualitative characteristics to numbers. He introduced the Orphipythagoria mysteries. He shaped the Pythagorean School of philosophy. The systemization of and the development of the eight-string music render Pythagoras as a true inventor of music. He introduced music for therapeutical reasons.
  • The astronomer and mathematician Aristarhos the Samian (390-330 BC) he was the first to make reference to the solar system and calculated distances between celestial bodies. He was the first to teach about the movement of Earth around its axis and around the sun.
  • The philosopher of the senses Epikouros lived in Samos throughout his childhood and teenage years.
  • Kallistratos who invented the 24-letter alphabet
  • The sculptor Pythagoras. Son of a Samian family, he was born in Rigio of Italy. The famous Iniohos, charioteer, of Delphi is considered to be one of its masterpieces.
During the Asian Campaign of Alexander the Great, Samos was an important army and naval base.

After the death of Alexander his successors, realizing Samoss key geographical position for the control of the west and southwest coasts of Asia Minor, fought for the islands domination.

With the victory of the Romans against the Macedonians in Kinos Kefalais, in 197 BC, Samos was declared independent as every other Greek city.
In 131 BC Samos was assigned along with the other Ionian cities to the Roman province of Asia.

Subsequent to the loss of its independence from the romans, Samos entered in an era of decadence. This state of things continued throughout the first period of the Byzantine Empire and even if the historical sources for this period are scarce, it is believed that the population of the island diminished dramatically. Samos was raided by pirates during the reign of Ioulianos (361-363 AD) by Goths, Alanans (5th century AD), Slavs (6th century AD) and Arab Saracens the 7th century.

The 7th century AD the heirs of Heraklios took over the administrative and military restructuring of the empire and created a mighty fleet. They introduced the institution of Themata. These were military units permanently stationed to different areas of the Empire responsible for its defense. Land was given to the soldiers so they did not only defend the Empire but their homes and land too. The 9th century AD the naval Thema of Samos was created, which controlled the opposite coasts of Asia Minor. The Thema of Samos took part in the campaigns against the Saracens and especially at the liberation of Crete from Nikiphoros Phokas the 961 AD.

In 1312 the Turks attack repeatedly the island and its inhabitants find security in the mountainous castles of Lazaros and Loulouda. After the disastrous earthquake of 1476 the inhabitants of the island flee from Samos.

In 1546 the French traveler Pier Belon passed through Samos and reported in his journal that he did not come across any village in the island and that there were only shepherds in the highlands.

The 1562 the sultans admiral Kilidz Pashas due to a sea storm unbarks in Samos. He was deeply impressed by the natural beauty of the island and after the erg of his officer Nikolaos Sarakinis from Patmos, he asked from the sultan to place the island under his control and to recolonize it.

With the sultans decree a lot of privileges were given to Christians who would colonize Samos and it was strictly forbidden for a Turk to inhabit the island or even stay there for a brief time. Greeks from all over Greece colonized the island. The names of their place of origin can still be found in the names of existing villages such as: Mitilinioi, Arvanites, Koumaioi from Kimi, Vourliotes from Vourla of Minor Asia, Pagondas from the village with the same name in Evoia, Moraitohori etc.

Thanks to the relative independence that the Hegemony assured, a new period of development began in Samos. The road system was built, the sector of public health and the education were organized and there was an important development of arts and sports.

In 1849 with the publishing of the New Administrative Charta the common law was redefined to a more liberal direction. The special political system of Samos was the cause for the development of social and political institutions different from those of other islands.

In 1837 the central school of Vathi was founded, a high school in Mitilinioi and other schools in the villages and in 1854 the central school of Vathi became the 1st Pythagorio High School.

Between 1842 until 1862 the new port of Tigani (Pythagorio) was built having as foundation the ancient port of Samos. In 1863 the first newspaper Samos was printed. All official decrees of the Hegemony were published by Samos.

From 1881 until 1912 there were continuous struggles for independence form the sultan. The 11th of November 1912 in the church of Agios Spiridonas the representatives of the people of Samos unanimously voted the unification of the island with Greece. The leading figure of the unification was Themistoklis Sophoulis. After 1900 the systematic cultivation of tobacco and vine begun. The exquisite Muscat wine of Samos was exported mainly in Germany, Holland and France while the tobacco in the USA and Germany. The tobacco industry flourished until the economic crisis of 1930. In 1932 there were public tobacco factories in the port of Vathi, in Tigani (Pythagorio) and in Neo Karlovassi. In Karlovassi 40 small and large leather factories were operating, employing 300-400 workers.

Throughout the era of sail ships Samos had an important role in this industry and with the arrival of the steamships the Atmoploia Samou was founded by the commercial house of Iglessis in 1910. The construction of ships had a notable development thanks to the Samian pinewood.

In 1932 small sail ships and mechanized, with internal combustion engines, were being built in different locations of the island. The most important were in Tigani (Pithagorio), in Marathokabos and in Kalabaktassi. It is estimated that Samos built half of the Greek fleet.

The port of Pithagorio linked Greece with the Dodecanese, which was under Italian occupation and all commerce with the coasts of Asia Minor was conducted through Pythagorio.

During the 2nd world war the Greek and allied forces used Pythagorio for their movement from and to Asia Minor. The people of Samos played a decisive role in the resistance against the German and Italian invaders. With the surrender of Italy the Italian commander of the Kouneo brigade placed his men under the command of Bishop Eirinaios and Greek forces (Ieros Lohos) and latter English forces come to the island from the Middle East.

1st-17th November 1943 elements of Ieros Lohos (The Sacred Band) parachuted successfully while others landed by sea in Samos and organized the defense of the island against the Germans.

The 17th of November 1943 bombarded Samos and especially Pythagorio the port used by the Italians. A lot of people fled to the Monastery of Spiliani. The germans conquered the island but the resistance continued on the mountains until the final liberation of the island.