The Minoan town now named Kydonia by many archaeologists has not been completely uncovered because it lies beneath the modern city of Chania. However a number of small sites have been excavated, the most important of which are on the low hill called Kastelli behind the former Turkish mosque which is situated on the harbour front.

The largest of these sites is in Ayia Aikaterini Square and it has been excavated by a joint Greek-Swedish team, led by Hallager and Tzedakis, for several decades. The excavations in the square revealed part of a Minoan town with four or possibly five houses around a square.

House 1 has been the most thoroughly excavated and this was built in LM IA and destroyed by fire in LM IB. The two wings of the building cover 212 square metres and it has 14 rooms. Among the rooms whose use has been identified there were a Minoan Hall, a kitchen, workrooms and storerooms in which a large amount of pottery was found.