The Archaeological Museum of Rethymnon is lodged in the pentagonal building just in front of the central gate of the Fortetza (eastern gate). The building had been constructed by the Ottomans to protect the entrance of the fort.

The exhibits come from various areas all over the prefecture and represent all the prehistoric and historic periods. The Late Neolithic (3500-2900 b.C.) and Early Minoan (2800-2100 b.C.) pottery, tools and statuettes, among them a violin-shaped marble figurine, have been found mainly in the caves of Melidoni and Gerani; the Middle Minoan (2100-1600 b.C.) finds come from the building complexes of Apodoulou and Monastiraki sites, as well as from the peak sanctuary at Vryssinas; what is most interesting is the great number of seal stones and the clay model of a shrine, preserved only in its upper part.

The Late Minoan (1600-1100 b.C.) period is represented by various finds, mainly from the cemeteries of the area, with most important this of Armeni; an impressive serrated helmet and a clay figurine of the well known "goddess with upraised hands", along with weapons, jewels, tools and abundant pottery are some of the most important exhibits.

One can also see finds of the Geometric (1000-700 b.C.), Archaic (700-500 b.C.) and Classical (500-300 b.C.) periods, from the sites of Eleutherna, Axos, Stavromenos and Argyroupolis, the most interesting being the funerary steles.

Finally, from the Hellenistic and Roman periods it is worth seeing the marble statue of Aphrodite (Venus), a Roman copy of the Greek original, as well as the glass vessels very common during the Roman period.