- The Archaeological museum of Rethymno, just opposite the entrance of the fortress, exhibits objects from the Neolithic to the Roman period, found at the prefecture of Rethymno. Clay figurines, funerary coffers, grave offerings, statues, grave steles, red-figure vases, bronze vessels, jewellery and glass vases, are some of the objects on display.
- Rethymno Centre of Contemporary Art, at 5, Himaras St.,below Fortezza, houses a permanent collection of modern local and Greek art. Since 1995 the gallery and the town of Rethymno have become a part of the National Cultural Network, set up to promote contemporary visual arts within an international framework. The gallery regularly organises or hosts exhibitions of Greek and foreign artists.
- The Historical and Folk Art museum of Rethymno, in a 17th century restored Venetian building, at 28-30, M. Vernardou St., just after Neratzes mosque. The museum is a non profit foundation, aiming to the research, collection and representation of the unique and exceptional rural and urban life of the Cretan people since the seventeenth century. It houses a folkloric collection of everyday-life objects, plus works of traditional art, in the likes of weaving, embroidery, lace, pottery, jewellery, farming, basketry, metal work, smith's tools and cooking. The historical collection consists of photographs, drawings, documents, coins and weapons.
- The Paleontological Museum. The Veli Pasha Mosque , with the peculiar architecture consisting of 9 domes and 13 adjacent cells, the "Priory" and its surroundings this is itself a monument of the city of Rethymno. Allocated to M.G.F.I. by the Ministry of Culture. Nowadays it serves as Paleontological Museum Annex M.G.F.I. Crete.
- The paleontological collection of the Municipality of Rethymno, allocated to the Museum, is the basis of the material. Visitors have the opportunity to meet a significant part of the evolution of Crete, geological and paleontological changes suffered in a long term 300 million years. Original findings of endemic mammals in representations of real size and anatomical arrangement surround presentation. Stand the Cretan dwarf elephants, hippos and dwarf polymorphs Cretan deer, particularly coryneform deer Rethymnon (Candiacervus ropalophorus), which forms the logo of the museum.
In suitably landscaped garden 2.5 acres already planted trees and plants that thrive in Crete as plane trees, sour orange, Judas, olives, carob, Cretan palms, oleanders and laurels and shrubs such as wild roses, arbutus, mastic trees, myrtle, lavender, dittany, osier, rosemary and agriolevanta.
- The Ecclesiastical Museum houses the old watch of the cathedral, garments, disks, coins, etc.