After the catastrophe of 1450 B.C. the town is rebuilt and continues to exist until the end of the minoan years (1100 B.C.) with intermittent minor catastrophes. In the post-minoan III period (1400-1100 B.C.) the town reaches very high prosperity. Its products are recognised at Knossos in Eastern Crete, in Thera, even in Cyprus. Its cemetery expands considerably round the settlement. Grave jars, subterranean vaulted graves carved in rock are discovered daily on the eastern, northeastern section of today's town.
During the first centuries of the lst millenium e.e. in the geometric and archaic years, architectural remains are not located, till now but only abundant ceramics, something which indicates that the town continued its life even during that period. Part of a frieze which is in the museum of Hania depicts the facade of a temple with the statue of the Goddess surrounded by archers. Very few finds suggest the existence of the town during the classical period (5th-4th century B.C.) However this period must have been an era of prosperity for the area according to the testimonies of ancient writers. The famous sculptor Krissilas, Phidias' pupil, came from Kydonia of the classical period. As far as the hellenistic period is concerned (end of 4th century B.C.-69 B.C.) there is enough evidence about the flourishing of the town. Houses with mosaic floor have been found in several parts of the town, which during .that period had expanded also beyond the hill of Kasteli.
Remarkable graves with rich finds survive during this period. 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 leader ship of Lasthenes and Pavares, fought the Romans heroically, but eventually they were defeated. The town con tinued its life and flourished during the Roman period. The town of Kydonia continued to flourish and in the early Byzantine period 321-823 A.D. Christianity spread from the 1st century and Kydonia is chosen as "seat of Bishop" and is often mentioned in Records of Councils and Ecclesiastical "Minutes" till the 9th century A.D.
As from this period we have very few archaeological indications, which are confined to a few tomb inscriptions from the church of St John and from the area of today's orphanage, which showed that they were extended cemeteries of the town.
From the Legend (biography of Saints) of St Nicholas the Confessor (abbot of the monastery Stoudiou and well-known apologist of icons) who came from Kydonia, we learn that his country was rich and prosperous and the memory of its glorious past is indelible. The events of the Arab attack are described in dark colours. The Arabs are ousted by the Byzantines in 961 A.D., but the town maintains its strategic significance. The Byzantines build a fortress, which in many parts rests on the ancient walls, with the building materials of ancient Kydonia.
The town however begins to decline. From this period only a few parts of the walls in Kasteli survive. In the first half of the l3th century the Venetians endeavour to establish their sovereignity in the area of Hania. After the siege of Constantinople by the Latins (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 characterised Piscatori as a pirate and after a tenacious war they exhiled him from the island. The possession, however, of the island by the Venetians did not occur immediately, but after hard fights against the indigenous population, particularly in the borough of Hania. The borough of Hania is divided into 90 "Cavaleries", which are 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 planning of the town within its boundaries. The public buildings develop along the central road Corso, (Today's Kanevaro Street) which crosses Kasteli. Hania develops into the second town of the "Kingdom of Crete" and is the seat of "Rector" and latin Bishop. The town and its port are the centre of a wealthy agricultural area with economical and political connections with Venice. In the middle of the 16th century the town is fortified once more, an operation based on designs by the Veronese mechanic Michele Sammichelli with contemporary walls and trench. The. fortification is enhanced with fortresses on the islets Thodorou, Souda and Gramboussa. Within the new boundaries the new town-planning network develops, which survives today Big public buildings are errected - temples, storerooms, shipyards, a lot of which are maintained even today. The architectural character of Hania is strongly Western with predominant the element of Venetian mannerism and some Flemish influences. Quite a few of the buildings of that period are maintained with many subsequent alterations.
In the middle of the l9th century Hania became the headquarters of Administration and with the revolution of 1847, the capital of the autonomous Cretan State. The town assumes a multinational character with the presence of Foreigh Leagues something that had consequences on the economical, social and cultural life. The architectural style changes according to the models of the West and 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 clamorous crowd of Turkish Cretans, Orthodox. indigenous Cretans, Beduins, Jews and Europeans gave Hania a special colour. The Cretan people however never stopped wishing and fighting for the unification of Crete with Greece. The yearning dream came true on the lst 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 till the flnal fall of Hania after a siege of 10 days. Hania gets bombed and the old town is completely destroyed. During the years of the occupation a strong resistance was organised against the conquerors, and this fact has made Hania one of the centres of organized resistance in Greece.