The fly collection includes true flies as well as midges and gnats. The hind wings of all flies have been converted into halteres. The collection mostly contains flies from the Palaearctic Region, Sri Lanka and Madagascar.
The fly collection in its current form is primarily the work of Fred Keiser, the former curator of the entomology collections (1955 – 1967). Numerous trips to increase his collection took him to places in Switzerland and abroad, including to Greece, Tunisia and Morocco. He made two extended research expeditions to Sri Lanka (1953/54) and Madagascar (1957/8).
The collection contains around 54,000 mainly dry mounted specimens representing 7,000 species. Of these, around 400 taxa are represented by primary types.