During the so called Historical Years, Kythonia seems to have been a powerful city-state, whose domain extended from Hania Bay to the feet of the White Mountains. Kythonia was constantly at war with other city-states such as Aptera, Falasarna and Polyrrinia. In 69 B.C. the Roman Consul Cointus Metellus defeated the Cretans and conquered Kythonia to which he granted the privileges of an independent city-state.

Kythonia reserved the right to mint its own coins until the 3rd century A.D. The Roman conquest put an end to the civil wars and a period of peace began, unique in the history of the island. The Kythonia of the Historical Years was of the same size as the city of Hania at the beginning of the 20th century.