The Archaeological Museum of Rethymnon is temporarily housed in the basilica of Agios Fragiskos (St Francis) in the old town of Rethymnon. From 1991 to 2015 it was housed in the pentagonal fort-building, opposite the main gate of the fortress Fortezza built by the Ottomans to protect the entrance to the castle and later used as prisons.

It hosts exhibits from various excavations around the prefecture of Rethymnon which represent all periods from the Neolithic Age to the Roman period. Among the most important exhibits of the museum is a urn depicting a hunting scene, a figurine of a Minoan goddess, a marble statue of Venus, the violin-shaped marble idol found in the cave if Gerani, a semi-enclosed clay vase with stem and a cap, a head of a terracotta female figurine and other significant findings