The Geology department is one of the youngest in the museum, staffed by three researchers. Its main focus is the geodiversity of the south Aegean and eastern Mediterranean region, dealing mainly with the individual geological features, the tectonics, the landscape response and the life appearance in the area. Scientific staff participates in research and management projects enhancing the importance of the geological substratum for natural environment and human presence.

Also, collaborates with international and local research institutions in fundamental geological studies. The department supports also the educational and informational activities of the museum and the University of Crete, as well as, the temporary and permanent exhibitions.