Chania goes back to Minoan age around 3650 to 1400 BC but some lately archeological evidence indicate that 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 ancient Greece. The first wave of settlers from mainland was by the Dorians who came around 1100 BC. Kydonia was constantly at war with other Cretan city-states such as Aptera, Falasarna and Polyrrinia. In 69 BC, the Roman Caecilius Matellus conquered Kydonia to which he granted the privileges of an independent city-state.
Byzantine and Arab era
Under the Arabs, the Christian population was persecuted and moved to the mountains. The Byzantine Empire retook the city in 961 AD. In this period the Arabic name of the city was changed into Greek Chania. Byzantines began to strongly fortify the city in order to prevent another Arab invasion, using materials from the ancient buildings of the area.
The Venetian era
After the 4th Crusade (1204) and the fall of Byzantium in the Greek area, Crete was given to Bonifacio, Marquess of 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 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. The city's name became La Canea and its 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 in 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.
However, the walls did not prevent the Ottoman army from occupying the city in 1645 after just two months' siege. The Ottomans landed near the Monastery of Gonia in Kissamos, which they burnt. They seized Chania on 2 August 1645. Many people died in the siege. Most churches were turned into mosques. The Muslims resided mainly in the eastern quarters, Kastelli and Splantzia, where they converted the Dominican church of St Nicholas into the central Sovereign's Mosque. They also built new mosques such as the Küçük Hasan Pasha Mosque or Yali Mosque on the harbor. Public baths and fountains were a feature of the Ottoman city.
In 1821, as Greeks rose against the Ottoman Empire, there were conflicts between Greeks and Muslims in Chania, leading to casualties from both sides, most of whom were Muslims. 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. This was when a large part of the local Muslim population was killed. There was no Muslim population left after the population exchange between Greece and Turkey in 1922.
In 1898, during the final moves towards independence and union with Greece the Great Powers made Chania the capital of the semi-autonomous Cretan State, 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, 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 the union with Greece which came after Eleftherios Venizelos's constant opposition to Prince George's rule over Crete. The series of conflicts includes the Therisos revolt 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) eventually led to Crete's union with Greece on 1 December 1913, following the Balkan Wars. The Greek flag was raised for the first time at Fort Firka in the Old Harbour in the presence of Venizelos and King Constantine.
World War II
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 stayed in a villa near the village of Perivolia outside Chania before escaping to Egypt. Part of the city was bombed and a significant proportion of the area's population 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, which was carrying most of the Jewish prisoners.