The Archaeological Museum of Rethymno occupies a building with its own remarkable story. Its current home is the Agios Frangiskos church, a former Franciscan monastery cathedral dating to the early 1500s, later absorbed into the Neratze mosque complex under Ottoman rule. From 1991 to 2015 it was housed in the Ravelin, a pentagonal fort-building beside the Fortezza.

Small in scale but rich in range, the collection spans Neolithic Crete through Minoan, Roman, Byzantine and Venetian periods. Highlights include Minoan sarcophagi decorated with deer and birds, an urn depicting a hunting scene, a figurine of a Minoan goddess, and a marble statue of Venus.

VoiceMap's self-guided audio tour of Rethymno's Venetian harbour and old town uses the museum to trace the city's layered past. They link Minoan finds to the Venetian and Ottoman buildings that still surround it.