The main focus is the bird collection with specimens from all over the world, with about ten percent of the globally described bird species represented in the collection. The mammal collection is considerably smaller than the bird collection and consists of habitus and skins, skeletons and hunting trophies. The majority of fish, amphibians and reptiles are liquid preparations.
The bird collection can be divided into three main categories - habitus specimens, skins and eggs. The egg collection is particularly dominant, with about 5,000 specimens of over 800 species. It originated in the 18th century and was expanded in 1866 with eggs of European birds from the natural resources dealer Keitel and in 2002 with a substantial enrichment from the Berlin-Friedrichsfelde Zoo. The egg collection from the estate of Hans Münch also includes about 800 specimens from 300 species, the identification of which was carried out by Max Schönwetter. Also preserved are specimens of the eagle owl Bubo bubo and the great bustard Otis tarda from Johann Friedrich von Beulwitz's collection, which he started in 1770. His records also provide valuable insights into the breeding birds of the Principality of Schwarzburg-Rudolstadt.
Stuffed specimens, dermoplastics and skins make up about 3,000 pieces, with the collection receiving a steady influx of specimens, especially from the regional bird fauna. A rare specimen in the collection is the habitus preparation of a male bald ibis Geronticus eremita. The animal was shot in 1910 in the Syrian oasis of Tudmur. Also noteworthy are two specimens of the Rock Sparrow Petronia petronia from Gumperda from 1907, a Common Loon Gavia immer from Thüringenhausen from 1907 and the Paddyfield Warbler Acrocephalus conchinens from Cuc Phuong National Park from 1995, which is considered the first record for Vietnam.
The collection of mammalogical objects with its approximately 3,500 specimens consists of habitus preparations, skins and skeletal material. Significant for Thuringia are the bat specimens, which were set up in the second half of the 19th century and are considered to be the oldest records. These are the water bat Myotis daubentonii, the greater mouse-eared bat Myotis myotis, the broad-winged bat Eptesicus serotinus as well as the two-coloured bat Vespertilio murinus and Barbastella barbastellus, which were collected near Rudolstadt and Schwarzburg. Two otter specimens testify to the former occurrence of this species (Lutra lutra) near Rudolstadt in the second half of the 19th century.
In the history of the museum's collection, more than 40 taxidermists left traces of their craft and skills. Particularly noteworthy are the works of Philipp Leopold Martin, who is not only considered a pioneer of the concept of nature conservation, but also made some large dermoplastics - a technique he perfected in his time - and skins for the Natural History Cabinet. Among them are a tiger Panthera tigris from 1878, a chimpanzee and orangutan. Martin also prepared several smaller animals, such as a giant glider. His high-quality works already reflected an immense attachment to nature and its vivid representation in the 19th century and mark a turning point in the taxidermy technique of vertebrates.