There are traces of human presence within the prefecture of Chania since the Neolithic age (6000-3500/2900 B.C.) mainly in caves, but also within the city of Chania and at Nerokourou.
During the Minoan centuries (2800-1100 B.C.), the most significant settlement was that on Kastelli Hill of Chania. Houses have been found also at Dembla of Varypetro, at Nea Roumata, Keramea, Pervolia, Sternes Akrotiri, Modi, Nerokourou, Nopegia, Falasarna, Kaledonia, Ravdoucha, Kasteli of Kissamos, Stylos and at Samona Apokoronos. During the mid-Minoan period (2000-1550 B.C.) the settlement of Chania developed into an agricultural, trade and marine centre. However, it reached its prime during the post-Minoan period (1550-1110 B.C.) where there is a town-planning design with building blocks and rich and well-kept houses, which used to have two floors.
A brief history of Chania. In 1450 B.C., the outbreak of a fire, perhaps due to war, destroyed the settlement of Kasteli, parts of which, however, were still used as residences subsequently. During the 3rd post-Minoan or Mycenaean period (1440-1100 B.C.), the entire prefecture reached its prime and Chania developed into a trade centre with relations tied with the Peloponnese, Boeotia, Cyprus, Phoenix and Egypt. The presence of the Mycenaeans is depicted in architecture and ceramics.
During the 12th century, most settlements were abandoned, perhaps due to decline, in combination with the appearance of the "people of the sea".In the beginning of the Iron Age (1st millennium B.C.) the Dorian arrived, who prevailed and integrated with the existing inhabitants. The geometric period began and city-states were established. During the 5th centuries, cities became more powerful. However, they flourished during the Hellenistic years (323-69 B.C.), despite the wars between them. The most important cities were those of Kydonia, Polichni, Pergamon and Keraea in the province of Kydonia, Polyrrenaea, Inachorion, Falasarna and Kissamos in the province of Kissamos, Aptera, Amphimala and Hydramia at Apokorona, Elyros, Lissos, Syia, Kandanos and Hyrtakina at Selino, Anopolis, Araden, Poekilasion and Tarra at Sfakia.
In 69-67 B.C., the Romans seized Crete. Despite that, however, the Cretan cities continued to flourish also during the Pax Romana period. In 58 A.D., Titus, the disciple of Saint Paul, became the first Bishop of Crete. Towards the end of the 4th century A.D., the whole island was Christianised and became subject to the East Roman State which evolved into the Byzantine Empire.
In 823 or 824 A.D., the Saracen seized Crete and destroyed many coastal cities of the prefecture. In 961 A.D., Nikephorus II Phocas liberated the island. To reinforce the shrinking population, Nikephorus II Phocas established his armies in the villages of Crete, as well as colonists from the Greek mainland and Asia Minor. Clergymen and missionaries, such as John Xenos, built churches and encouraged the Christian spirit in the inhabitants. In 1082 and according to tradition, Byzantium established 12 nobles ("Archontopoula") on the island, who became the foundation of aristocracy, especially in western Crete.
In 1204, following the Fall of Constantinople by the Crusaders, Crete fell under the Venetians who, until 1211, were in dispute with the Genoese over its ownership. However, full dominance over the region of Chania took place only in 1252 when the land was divided amongst the colonists from Venice; the city was restructured and it became the headquarters of Rector (ruler) of the prefecture.
The Venetians enforced Catholicism, abolishing orthodox bishops and suppressing the local population, which frequently rebelled with the support mainly of the Palaeologo family of Constantinople: (1211, 1219, 1224, 1228-33, 1272-78, 1283-1289, 1332,1341, 1363-1364, 1365). With the overthrow, however, of Byzantine in 1453, the rebels lost all support. The prevalence of the Turks in the Aegean and the loss of Cyprus in 1570, change the attitude of the Venetians towards the Greek population of Crete and brought it to their side in view of a future conflict with the Turks. That is how the only great Kantanoleo revolution during the 15th and 17th centuries took place in 1527. The new status led to the intercommunion of the Venetians with the locals, to the development of urban classes, the improvement of the economy and to the flourishing of literature and arts, which is known as the Cretan Renaissance. Orthodox monasteries were built or renovated within the prefecture of Chania, prominent clergymen and scholars were active and noteworthy icon painters appeared.
In 1645, the Turks in Gonia of Kissamos and after a two-month siege, took over Chania. This is when the Turkish rule began with the Islamization of part of the population, depredation of the lowlands and restriction of the freedom of the "ragias" people.
In 1770, Daskalogiannis rebelled at Sfakia with the encouragement of Russia. However, the rest of Crete did not revolt and the revolution was suppressed with villages in the province being destroyed.
In 1821, Crete participated in the great revolution with significant victories and constraining the Turks to the forts. Hussein bey, however, won in a series of battles with the Cretans with the assistance of an Egyptian fleet and turned their actions into a war of klephts (1823-1824). With the siege of Grambousa in 1825, a new rebel period began but which, although lasting until 1830, did not place Crete within the established Greek state. Crete was then offered to Egypt in exchange for its assistance to Turkey.
During the Egyptian rule (1830-1841), a heavy tax was imposed on the people, who suffered greatly under the arbitrariness of the Egyptians. When Crete was re-seized by Turkey, a new revolution broke out, the so called "Haerete" (1841), which was suppressed by powerful forces. In 1850, the headquarters of the Turkish ruler was transferred from Heraklion to Chania.
In April of 1858, five thousand armed Cretans gathered at Boutsounaria and demanded the abolishment of oppressive measures (Mavrogenis movement). The Gate was forced to satisfy most of their demands.
The second greatest revolution began in 1866 and continued until 1869; the monastery of Arcadio was blasted and became the highlight of the revolution. This revolution forced the Turks to proceed with administrative reforms (Constitutional Law). In 1878 a new rebellion led to the Treaty of Halepa, which conceded significant privileges to the Cretans and appointed a Christian Governor for the island. In 1889, due to political divisions of the Christian population and the unilateral proclamation of the Union by a portion of rebels, Turkey abolished many of these privileges. A five-year period of terror and oppression followed which led the Cretans once more in 1895 to rebel under the leadership of the Commission for Political Changeover and aiming at the island's autonomy. The defeat of the Turks at Vamo was partially the cause of massacres at Chania (May 11, 1896), as well as in other areas of the prefecture, which ceased by intervention of the Great Forces.
With the new massacre and the burning down of a Christian suburb at Chania on January 23 and 24 of 1897, the revolution of the Cretan was revived with the purpose of uniting with Greece. The Greek government sent an expeditionary army of 1500 men to Crete, which after its first success, was prohibited by the Forces to approach Chania. The refusal of the rebels at Akrotiri to comply with the instructions of the European Admirals caused them to be bombed by the Forces' battle ships (February 9, 1899). The defeat of Greece in the Greek-Turkish war in 1897 and the refusal of the Europeans to accept a union, forced Eleftherios Venizelos and other leaders of the revolution to accept the solution of autonomy.
In December 1898, Prince George of Greece arrived at Chania, representing the Great Forces and as governor of the autonomous Cretan State. His disagreement with Eleftherios Venizelos on the method of governance over Crete and on the issue of union, led to the Therissos revolution (1905) which resulted in the prince's departure and his replacement by Alexander Zaimis. The election of Venizelos as prime-minister of Greece in 1910 and the victorious Balkan Wars in 1912-1913 opened the way for the union of Crete with Greece, which was made official with the raising of the Greek flag at Firka of Chania on December 1, 1913.
Since then, Crete, being part of the Greek state, has participated in the adventures of Hellenism. On May 20, 1941, it was invaded by German paratroopers. Following a heroic defence which lasted 10 days, in which, apart from British and Greek armies, Cretan citizens participated with primitive weapons, the island was seized and suffered a harsh rule with executions, hostages and destruction of villages. Nevertheless, rebel forces fought against the invader until July 1945, when the last of the Germans departed from the region of Chania.