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Early history. A clay figurine found in a tomb (4th-3rd century B.C.)Chania is the site of the Minoan settlement the Greeks called Cydonia, Greek for quince. Some important evidence for the existence of this Minoan city below some parts of today's Chania was found by excavations in the district of Kasteli in the Old Town. This area appears to have been inhabited since the Neolithic era. The city reemerged after the end of the Minoan period as an important city-state in Classical Greece, one whose domain extended from Hania Bay to the feet of the White Mountains

The first major wave of settlers from mainland Greece was by the Dorian Greeks who came around 1100 BC. Cydonia was constantly at war with other Cretan city-states such as Aptera, Falasarna and Polyrrinia and was important enough for the Cydonians to be mentioned in Homer's Odyssey (iii.330). In 69 BC the Roman Consul Metellus defeated the Cretans and conquered Cydonia to which he granted the privileges of an independent city-state. Cydonia reserved the right to mint its own coins until the third century AD.

Byzantine Era
Further information: Byzantine Greece
The early Christian period under Byzantine rule (First Byzantine Period, 395 - 824 AD) and the rule of the Arabs, who called the settlement Chania, are not well documented. During the former, Christianity spread in the island but during the latter, the Christian population was persecuted and moved to the mountains. The Byzantine Empire retook the city in 961 AD (Second Byzantine Period, until 1204 AD). They began to strongly fortify the city in order to prevent another Arab invasion, using materials from the ancient buildings of the area. By this time Chania was the seat of a bishop.

The Venetian era
 The old harbour during the Venetian eraAfter the Fourth Crusade (1204) and the fall of the Byzantium in the Hellenic area, Crete was given to Bonifacio, marchese de Montferrat. He, in turn, chose to sell it to the Venetians for 100 silver marks. In 1252 the Venetians managed to subdue the Cretans but in 1263, their rivals of Genoa, with local support, seized the city under the leadership of Enrico Pescatore, count of Malta, and held it until 1285, when the Venetians returned. Chania was chosen as the seat of the Rector (Administrator General) of the region and flourished as a significant commercial centre of a fertile agricultural region.

The Venetian rule was initially strict and oppressive but slowly the relations between the two parts improved. Contact with Venice led to close intertwining of Cretan and Venetian cultures, without, however, the Cretans losing their Greek Orthodox nature. The city's name became La Canea and fortifications were strengthened, giving Chania the form that it still has today. On the other hand, after the fall of Constantinople in 1453, many priests, monks and artists took refuge to Crete and reinforced the Byzantine religion and culture on the island. The city of Chania during the period that followed was a blend of Byzantine, Venetian and Classical Greek cultural elements. Many of the important buildings of the town were built during this era and the intellectual activities (written word, music, education) were also promoted.

Ottoman Era
 The old harbour during the Ottoman eraFurther information: Ottoman Greece
However the walls did not prevent the Turkish army overrunning the city in 1645 after just two months' siege. The Turks landed near the Monastery of Gonia in Kissamos, which they plundered and burnt.[citation needed] They seized Chania itself on 2 August 1645. Huge numbers died in the siege, particularly Turks. The Turkish commander was executed on returning home for losing up to 40,000 men. Later, most churches were turned into mosques and the riches of the city were taken. The Turks resided mainly in the eastern quarters, Kastelli and Splantzia, where they converted the Dominican church of St Nicholas into the central Sovereign's Mosque ("Houghiar Tzamissi"). They also built new mosques such as "Kioutsouk Hassan Tzamissi" on the harbour. Public baths - Hamam, and fountains were a feature of the Turkish city. The pasha of Crete resided in Chania.

In 1821, as Greece rose against the Ottoman Empire, there were conflicts between Greeks and Turks in Chania, leading to casualties from both sides, most of which were Christians though. The Bishop of Kissamos, Melhisedek Despotakis was hanged from a tree in Splantzia for participation in the revolutionary events. In 1878, the Pact of Halepa was signed and Christians were granted certain rights. This was when a big part of the local muslim population moved to Turkey. The rest of them stayed until the Population exchange between Greece and Turkey in 1922.

Modern Greek Era

Further information: History of Modern Greece
Eleftherios Venizelos, who hailed from Mournies near Chania, was the leader of the 1896-97 uprising against Ottoman rule and went on to be Prime Minister of Greece and a great statesman. His tomb is on a hill overlooking Chania (Profitis Ilias). In 1898, during the final moves towards independence and enosis— union with Greece— the Great Powers made Chania the capital of the semi-autonomous Cretan State ("Kritiki Politeia"), with Prince George of Greece, the High Commissioner of Crete living here. During these years Crete issued its own stamps and money. This was a very important transitional period when, no longer an isolated vilayet of the Ottoman Empire, the city became more cosmopolitan and flourishing, regaining its role as the crossroad of civilizations, influenced by Europe as well as by the East. Many important buildings were built during this era, intellectual and artistic societies were created and a new class of local aristocracy brought a different atmosphere to the everyday life of the town. The district of Halepa has many fine neoclassical embassies and consulates dating from this period.

However the main goal was enosis with Greece which came after Venizelos's constant opposition to Prince George's rule over Crete. The series of conflicts includes the Revolution of Therissos in 1905, which overthrew Prince George and brought Alexandros Zaimis to rule Crete. Finally in 1908 Venizelos managed to establish a revolutionary government, recognized by the Great Powers. His later election as the prime minister of Greece (1910) was the last step before Crete was united with Greece on the 1 December 1913. The Greek flag was raised for the first time at Fort Firca in the Old Harbour in the presence of Eleftherios Venizelos and King Constantine.

Chania in World War II
Further information: Axis occupation of Greece during World War II and Battle of Crete
Another important period for the city of Chania was the invasion and occupation by German forces during World War II. The British force that faced the German paratroopers during the Battle Of Crete in 1941, had artillery elements over the hill of Dexameni in the south of the city. These elements bombed the German forces in the Maleme airfield undetected, until they ran out of ammunition.George II of Greece also, stayed in a villa near the village of Perivolia, outside Chania before he escaped to Egypt. Part of the city was bombed, progress in several aspects of life was halted and a significant proportion of the area's human potential was either executed or imprisoned due to participation in the resistance against the German rule. The Jewish community of Chania was also eliminated during the German occupation. Most of them were transported off the island by the Nazi occupiers in 1944. Tragically a British torpedo sank the ship "Tanais" carrying most of the Jewish prisoners, killing the island's pre-war community.

Modern Era
Fortunately, Chania and Crete in general escaped the disastrous consequences of the Greek Civil War of the postwar years. The city of Chania was slowly regaining its normal pace of development during the 1950s, trying to overcome the difficulties that the war had left as an aftermath. During the 1970s Crete became a major tourist destination for Greek and international tourists, something that gave a significant boost to the city's economy and affected the everyday life and the overall culture of the locals. The capital of Crete was moved to Heraklion in 1971.