The Prefecture of Chania has a long history since the first signs of life on the land is dated to Neolithic times. In the following years Kydonia grew on whose ruins the present day capital of the prefecture is built. In the following years a strong presence was made by the Arab conquerors in 824 B.C. who renamed the city to Al Hanim from where its present day name comes from. From 961 to 1204 A.D. the prefecture as well as the whole island for that matter went under Byzantine rule. In 1645 however, the Turks occupied the whole prefecture apart from Sfakia and annexed it to the Ottoman Empire until 1825 when the promontory of Gramvousa becomes the center of the revolutionary nucleus and the revolution spreads throughout all of Crete.
In the decade 1830-1840 Crete went under the rule of the Egyptians. In 1905 it was roused by the Theriso rebellion with Venizelo as leader requesting union with Greece which was realized in 1913.