The church of Saint Francis is one of the most important monuments of Rethymno. It was the main temple of the Monastery of the Franciscan Order. The architecture of the building - a single aisle Basilica type with wooden roof - and its ornaments are very interesting. Next to the east side of the temple two deserted chapels are preserved. Its Corinthian style main doorway is impressive, with capitals of composite order. During recent excavations around the church valuable archeological findings have been discovered, including two tombs of Venetian nobles.
During the Turkish occupation the temple was turned into an "Imaret" (a shelter for the poor).
It was also used as a cultural center until 1996. It was recently renovated to accommodate the Byzantine and Post-Byzantine Collection of the Prefecture of Rethymno.