Scholars have been trying for years to analyse the etymology of the name "Hania," and to decide on the time when the name was changed from "Kythonia" to "Hania". The new name is first met as "Cania" in the document "Sexteriorum Cretensiu in Militias divisio" in 1211. Then the name "Canea" is mentioned in the document which relinquishes the Hania area to the Venicians in 1252. As for the change of the name from "Kythonia" to "Hania", the most convincing point of view is that of Prof. N. Platonas, who associates it with the existence of a big village "Alhania", named after the God "Valhanos" (Vulcan). The Sarasin Arabs found this name easier to use but confused it with their own word "Al Hanim" (the Inn). After the departure of the Arabs, the syllable "Al", probably taken to be the Arab article "Al" (the), was dropped when the name was translated into the Greek "Hania" and the Latin "Canea".

Historically and Archaelogically, the hill of Kasteli is one of the most significant parts of the city, as it has been inhabited since Neolithic times. The factors which contributed to the uninterrupted use of Kasteli as a residential area were : its geographic position and the fertile plain on the south, both of which contributed to making the district an important commercial and transport junction. Excavations have brought to light remains dating from the first Minoan period (2800-2000 B.C.). The houses of that period are large with well constructed rooms. The walls and floors are painted with a bright red colour. The Kasteli area was also inhabited in the Post-Minoan period (1580/1550 - 1100 B.C.).

According to the evidence offered by the clay tablets in Linear A scripture found on the hill, the area was reserved for royal use. Between 1380 and 1100 B.C. it developed into a commercial centre which was in constant communication with the rest of Crete and Greece.A historically significant ceramics workshop, known as "the Kythonia Workshop" has also been found in the Hania area. It now belongs to the post-royal period.

The Historical Years (1st millenium B.C.)
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 nad 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.

First Byzantine Period, 3rd Century A.D. - 823
Information about the Kythonia of the Christian Years is limited. The most important archeological finds are those of the remains of a Basilica, discovered recently near the Venician Cathedral in the centre of Kasteli. Various sources mention the Kythonia Diocese and the Bishop Kythonios, who participated in the Sardinian Synod in 343. Kythonia is mentiond among the 22 most important cities of Crete in the "Document of Ieroklis" in the 6th Century. The Kytonia Diocese is also mentioned in all the "Ecclesiastical Minutes" (taktica), before and after the Arabian Occupation.

The Arabian Occupation (823-961)
The occupation of Crete by the Arabs was effected gradually from 821 to 824. The consequences of the arrival of the Arabs in Crete were rather painful for the local population, who were subjected to a long and horrible period of slavery, resulting in the alienation of Crete from the Byzantine empire. St. Nicholas Stouthitis was born in 763 in Kythonia, which he left at the age of 10 to go to Constantinople. In 961, Nikiforos Fokas managed to free Crete and bring it back under the control of the Byzantine empire.

The Byzantine Period (961-1204)
The first action of the Byzantine empire, after reconquering Crete, was to re-establish their authority and power. Not only should all traces of the Arab occupation be abolished but also the defense of the island had to be organised quickly in order to avoid any Arab attempt to take back the island. Thus, strong fortifications are constructed along the coast and at strategic positions. The hill of Kasteli is fortified with a wall along its perimeter. This was constructed with building materials taken from the ancient city. It is still regarded as a remarkable military accomplishment and a proof of the continuous existence of the city in the period between the Arab and the Venician occupations.