The Museum has been housed in the church of the Venetian Monastery of St Francis since 1963.
The exhibits illustrate the cultural history and character of the area through the ages, from the Neolithic period to the Roman era. The exhibition hall is divided widthwise into two major sections. The east wing contains finds of the Late Neolithic period and the Bronze Age (Minoan era), while the west wing presents antiquities dated to the Iron Age (Historic era). The finds are presented in excavation groups and thematic units. The collections comprise Minoan finds from the city of Chania, prehistoric finds from caves, Minoan finds from various parts of the Prefecture, finds from tombs of the Geometric period, finds of the Historic era from Chania and various other towns and cities in the Prefecture, coins, prehistoric and historic jewellery, sculptures, inscriptions, stelai and mosaics.