The Romans were well aware of the strategic importance of the island of Crete and its conquest would open the way to the East. Rome had attempted to conquer Crete but was defeated in 71 B.C. Kydonia was the first city that confronted the Roman army. Despite its strong resistance, the city was finally conquered by the Romans. The Roman General Cointos Kaikilios Metellos the Cretan, as he was called after his victory, managed to conquer Kydonia in 69 B.C, and shortly after, the whole island of Crete. There is evidence that during this period there were luxurious public and private buildings, and excavations have revealed numerous sculptures and mosaic floors in different parts of the city. The ancient theater of the city was preserved until 1583 when it was demolished by the Venetians to use the building material for the construction of the city walls.

Finally, the initial construction of the "Byzantine" wall of the acropolis of Kasteli was probably built during this period. The necropolis of the city of Kydonia was spread around it. During the post-Roman years, Kydonia was still the greatest city of the region and for this reason it hosted the headquarters of the paleo-Christian Episcope. The recent discovery of a large paleo-Christian Basilica under the foundations of a Venetian Cathedral temple in the district of Kasteli indicates that Kasteli was probably the center of the city during this period.