According to archaeological finds the town of Hania was built on the ruins of a big ancient town – Kydonia.  Its name is read KY-DO-NI-JA on a Knossos tablet of Linear B Scripture.  According to Diodoros Sikeliotes Kydonia was founded by King Minos and was one of three big towns in Crete.
The Kasteli Hill (east of the port)) was in an ideal position for prehistoric settlements due to the fact that it was adjacent to the sea.. Surviving architectural remains from big buildings come from the early Minoan period (1900-2200 B.C.). The settlements developed and evolved into an important center in the first middle-Minoan period (200-1580 B.C.), at which point a Minoan colony was founded, beyond the Kasteli Hill. In 1450 B.C. this colony was destroyed by a big fire. Greek-Swedish excavations that began in 1967 uncovered buildings of this period with many rooms, several had floors paved with flagstones, second storeys and monumental entrances looking onto narrow streets. About 100 clay tablets with symbols of the Minoan Linear A Scripture that were found indicate the possible existence of a palace. After the catastrophe of 1450 B.C., the town was rebuilt and continued to survive until the end of the Minoan years (1100 B.C.) not without intermittent minor catastrophes. In the post-Minoan III period (1400-1100 B.C.) it became very prosperous. Its products were renowned in Knossos (Eastern Crete), in Thera, even in Cyprus. Its cemetery expands considerably all around the settlement. Earthenware burial jars and subterranean vaulted graves carved in rock were discovered daily in the eastern, north-eastern section of the modern city.
During the first centuries of the 1st millennium, namely in the geometric and archaic years, architectural remains have not been found until recently, only abundant ceramics which indicate that the town continued its life even during that period. Part of a frieze, now in the Museum of Hania, depicts the facade of a temple with the statue of the Goddess surrounded by archers. The very few remains that have been found suggest that the town existed during the classical period (5th-4th century B.C.). However, according to testimonies of ancient writers this period must have been an era of prosperity for the area. The famous sculptor Krissilas, Phidias’ pupil, comes from Kydonia during the classical period. As far as the Hellenistic period is concerned (end of 4th century 69 B.C.) there is enough evidence about the prosperity of the town. Houses with mosaic floors have been found in several parts of the town, which at the time had expanded beyond the hill of Kasteli. Remarkable graves with rich findings of this period have survived. In 69 B.C., the Romans declared war against Kydonia, and sent Consul Cointus Concillius Metellus to seize it. The people of Kydonia, under the leadership of Lasthenes and Pavares, fought the Romans heroically, but eventually were defeated. The town continued its life, and flourished during the Roman period.
Kydonia continued to thrive in the early Byzantine period - 324-823 A.D. From the 1 st century, Christianity was spreading and Kydonia was chosen as a “Seat of the Bishop”. It is often mentioned in Council Records and Ecclesiastical “Minutes” up to the 9th century A.D. Few archaeological finds remain from that period, these consist of a few tomb inscriptions from the Church of St John and from the area of today’s orphanage which indicates that there were extensive cemeteries in the town.

The period 821-961 A.D. was a dark period for Kydonia. The town falls into the hands of the Arabs after a siege. Historical sources of this period are not very clear and archaeological remains have not been found.  From the Biography of Saints the Legend of St Nicholas the Confessor (Abbot of the Monastery Stoudiou and well-known advocate of icons) who comes from Kydonia, we learn that his fatherland was rich and prosperous and the memory of its glorious past is indelible. The events of the Arab attack are darkly described. The Arabs are ousted by the Byzantines in 961 A.D., but the town maintains its strategic significance. With building materials from ancient Kydonia the Byzantines build a fortress which rests in many parts on the ancient walls.  The town however begins to decline and only a few parts of the walls in Kasteli survive from this period. In the first half of the 13th century, the Venetians endeavour to establish their sovereignty in the area of Hania. After the siege of Constantinople by the Latin people (1204 A.D.), Crete is ceded to Bonifatio Marques Momferato, from whom the Venetians bought the island. Bonifatio did not have time to seize Crete before its sale to the Venetians, because the Genovian Count of Malta, Erico Piscatori, rushed and seized Hania and fortified the Acropolis of Kydonia. After its purchase by the Venetians, the latter characterized Piscatori as a pirate and after a tenacious war they exiled him from the island. The possession pouf the island by the Venetians did not occur immediately, only after difficult battles against the indigenous population, particularly in the borough of Hania.
The borough of Hania was divided into 90 “Cavaleries” that were given to the Venetian colonists, with the specific obligation to rebuild the town of Hania. It is they who repair the walls of Kasteli, and organize the town plan within its boundaries.
The public buildings develop along the central road Corso (today's Kanevaro Street) that crosses Kasteli. Hania develops into the second significant town of the “Kingdom of Crete” and is the Seat of the “Rector” and Latin Bishop. The town and its port becomes the centre of a wealthy agricultural area with economic and political connections with Venice. In the middle of the 16th century, the town is fortified once more, based on designs by the Veronese mechanical engineer Michele Sammichelli, with contemporary walls and trenches. The fortification was enhanced with fortresses on the islands Thodorou, Souda and Gramvousa. Within the new boundaries, the new town-planning network develops, which still remains today. Big public buildings were erected - temples, storerooms, shipyards (a lot of which are still remaining).  The architectural character of Hania is mainly Western in which the Venetian style predominates and with some Flemish influences.  Many of the buildings of that period have been preserved with many subsequent alterations.

In August 1645, the Turks seized Hania and the town was declared as the Seat of the Turkish Pasha, while an Orthodox Bishop of Kydonia was installed with the Temple of St Anargiri as his seat. The Catholic churches are turned into mosques and many new mosques also built. The conquerors are strongly influenced by the local architectural tradition, adding only certain functional and artistic elements. The town maintains the same structure, while the buildings assume some oriental character (wooden kiosks, wooden walls, tile roofs, latticed windows, a wide range of colours and cavities). In 1821, before the start of the revolution, the population of Hania had 10.600 inhabitants - 8.000 of them were Turkish and 2.600 Christians. However, in the last official census taken in 1881 of Cretan inhabitants during the Turkish domination - Hania had 13.812 inhabitants - 9.469 of them were Turkish, 3.477 Christian Orthodox, 159 Catholics, 5 Protestants, 4 Armenians and 485 Jews. The town of Hania was divided into 9 districts that constituted electoral sections - (1) Tophana, (2) Yousouf Pasha, (3) Arab Tzamissi, (4) Kasteli or Moussa Pasha, (5) Agha (6) Djejire Kolou, (7) Houghiar Tzamissi (Splantzia), (8) Koum-Kapissi and (9) Topalti. Since the siege of Hania in 1645 until 1830 Crete was governed by three Pashas, whose headquarters were in Hania, Rethymnon and Heraklion. From 1830, during Giritli Mustapha Pasha's administration, and until the end of the Turkish occupation, Crete was governed by a General Administrator (Vali) whose seat was in Hania. From 1645 until 1830, Hania had been governed by 196 Pashas. From 1830 and until the end of 1897 Hania and the whole of Crete had been governed by 37 Pashas and only 7 of them were Christians. Hania officially became the capital of Crete in 1849. In the middle of the 19th century, Hania became the headquarters of Administration and after the revolution of 1847 the capital of the autonomous Cretan State. By then, the town assumes a multinational character with the presence of foreign leagues, with many consequences on the economic, social and cultural life. The architectural style changes according to Western models, houses and mansions are built inside the walls as well as outside - on the outskirts of the town.
A creative spirit spreads from Hania to the whole of Crete, laying the foundations of order, security and prosperity. A bustling crowd of Turkish Cretans, Orthodox indigenous Cretans, Beduins, Jews and Europeans gave Hania a special colour. The Cretan people however never stopped hoping and fighting for the unification of Crete with Greece. This yearning dream came true on the 1st December 1913 in the presence of King Constantine and the leader of the revolution of Therisso (1905) Eleftherios Venizelos.

During the Second World War violent battles took place on the outskirts of the town until the final fall of Hania, after a 10 day siege. Hania is bombed and the old town is completely destroyed. During the years of the occupation a strong resistance was organized against the conquerors, and this has made Hania one of the centers of organized resistance in Greece.