The collection comprises all major groups of fishes and amphibians from the Palaeozoic, Mesozoic and Caenozoic as well as a histological thin section collection. There is a special collection of approximately 5,000 otolith specimens from fishes.

The collection of fossil fishes comprises approximately 25,000 specimens, which makes it the second largest vertebrate collection at the Museum, after the Mammals Collection. Its scope and composition make the sub-collection of fossil fish particularly attractive to scientists and contribute to its high international significance. The amphibian collection has 1,500 specimens. Although it is considerably smaller, it is no less interesting for research, due to the many types and originals as well as fossil growth series that show the development from a larva to an adult animal. Both collections include a total of 750 types and over 1,600 originals.

For historical reasons, many finds in the collection originate from Central Europe, especially Germany, such as Solnhofen – Upper Jurassic, Odernheim – Lower Permian or Bad Wildungen – Upper Devonian. The Baltic countries and Scotland are also strongly represented with numerous Devonian finds. Some parts of the collection hail from different parts of the world, e.g. the Canadian Arctic (Devonian), the USA and the Czech Republic (Upper Carboniferous), Lebanon and Brazil (Lower Cretaceous).