The first traces of habitation in the prefecture are placed in the Neolithic Age mainly on the south shore. Its highest point of growth is noted during the Copper Age. It is the age of Minoan civilization. This is when the first large palaces in Knossos and Phaistos are built, around which the cities are created and trade and shipping flourish.
In the 15th century B.C. the Minoan centers are destroyed by the explosion of the volcano of Thira. Activity continued; however, with a small decline. In the 11th century B.C. they invaded Doris where they were assimilated with the native inhabitants. After the 6th century B.C. the decline was evident and the prefecture exhibited no cultural growth. In 69 B.C. it became a part of the Roman province while in 395 it was taken under the control of the Byzantines. After the fall of Constantinople it was given to the Venetians. All of the prefecture then showed great economic and spiritual growth.
In 1669, it fell into the hands of the Turks, which with the heavy taxation and the continuous humiliation at the expense of the Christians subjected cruel living conditions onto the Cretans. The moment of freedom came in 1913, after struggles that lasted many years and after many revolts, with Eleftherios Venizelos as head.