The Centre of Archaeozoology, created by Louis Chaix in 1979, became a department of the Museum in 1982. Since 2002, the department of Archaeozoology is supervised by Jacqueline Studer.
It is the most recent of the eight research departments of the Museum, although the oldest faunal collections were already assembled and studied at the beginning of the 20th century by researchers working in the Museum of Geneva like Pierre Revilliod (1883-1954), Louis Reverdin (1894-1933) and Emile Dottrens (1900-1990). Swiss dwelling sites provide the majority of these old collections, for example Saint-Aubin, Cortaillod or Lüscherz.

Archaeozoology is the study of animal remains found in archaeological sites. The chronology covers all of the Quaternary, from the dawn of humankind about 2 million years ago to Modern times. The material essentially consists of bones, teeth, antlers and shells, but occasionally also softer parts of animals like hair, chitin, coprolites (ancient excrement), etc. First, this material must be identified to allow quantification of the different species that are present and their relative abundance. Then, following the measurement of the bones, the weight and size of the animals are estimated. Estimation of age profiles and sex ratios contribute to our understanding of human subsistence or husbandry strategies.
Archaeozoological research covers a large range of topics. The most common are hunting, fishing and husbandry undertaken by ancient populations. Slaughtered animals are used by humans as food, for manufacture of bone artefacts or for symbolic purposes. Archaeozoology is also concerned with the evolution of wild and domesticated animals, the different uses of live animals and the role they played in the development of human belief systems. Reconstructing the past environment is another goal. Finally, studying the location of the animal bones can aid in understanding the use of space in archaeological sites.
The Swiss researcher, Ludwig Rütimeyer, published in 1860 an analysis of bone remains that is considered as the first archaeozoological work (as opposed to palaeontology or comparative anatomy). This famous researcher studied thousands of bones collected from Swiss dwelling sites dating to the Neolithic and Bronze Age periods. He was able to identify about thirty species of mammals, twenty birds, some reptiles and nine fish species; he described the animal exploitation in each period, compared them and recognised an evolution in the diversity of fauna, frequency and size from the Neolithic to Modern times.