330 – 1204 μ.Χ.
In 330 Crete is released by the Romans and annexed to the Byzantine Empire. It was an independent administrative region, and was defined as a military and administrative center of the island Gortyn. At the head of the administration was a Byzantine general, who was asked to face the pirates who caused a considerable damage to the island’s economy.
During the Byzantine period Kydonia maintained its important position in Crete and watched closely all the developments related to the Church. By the early Christian era, was founded the Kydonia bishopric, which bishop participated along with other bishops of the island at the Council of Sardica (Sofia) in 342-343. The Church was under the jurisdiction of the bishop of Gortyni and from the late 9th century under the bishop of Candia (Heraklion).
Regarding the installation of the cathedral, an archaeological research has uncovered remains of a big church in place of the Venetian Cathedral of the Virgin in the center of the hill of Kastelli. Probably this temple was the bishopric of Kydonia.
In the 7th century, the Byzantines, in order to protect Chania from the Saracens, fortified the hill of Kastelli with the so-called “Byzantine Wall”. They dug a trench and constructed a wall around the hill converting it to an island.
Unfortunately, this was not enough to prevent the attack of the Arabs. The Saracens occupied Crete in 824 and in 828 Kydonia was destroyed. The period of Arab rule (824-961) was painful for the whole island, as it suffered from predatory and pirate raids. There is no archaeological evidence for these years, but we know that in this period lived Saint Nicholas the Studite, who was born in the Kydonia in 793 and when he was 10 years old he moved to Istanbul.
In 961 the Byzantines reoccupied the island and the city begun again to play the important economic and commercial role thanks to the port, although it was possible to move to a more secure area and specifically the new fortress “Kastelli”, built near Varipetro. At that time the bishopric was transferred from Chania to Agia and the Byzantine church of the Dormition converted into a cathedral of Kydonia.
The Byzantines had as main objective the restoration of economic, social and religious tranquility on the island. For that reason they brought noble families from Constantinople, while urging the reconstruction of many churches. Among these was the monastery of St. John the Theologian on the ruins of ancient Aptera.