The Museum of Biology is categorized as special museum which is for educational purposes focusing in biological education. The flora collections consist of wet and dry herbarium. It also has various collections of fauna in the form of wet preserves, taxidermy and skeletons. Some of these collections come from Indonesia, in addition to those coming from abroad which are donated by researchers, lecturers and people. Some collections are protected and rare fauna, such as Komodo, tigers, sun bears, pangolins, cendrawasih birds and eagles.
The collections of the museum are means of education for public. Visitors can gain knowledge about of flora and fauna diversities through direct observation to collections, completed with supporting information.
The collections of fauna are displayed in several thematic dioramas that describe their habitat conditions in nature. Various collections of animal skeletons will also knowledge-enriching for the visitors. The skeleton of an elephant named Nyi Bodro previously owned by the Palace of Yogyakarta Hadiningrat, Javan rhinoceros, dugongs, horses and waladis are some of flagship collections of the museum.
Collection of flora are displayed in the form of wet and dry herbariums. The Simplisia collection in the form of local grains and medicinal plants representing tradition and culture is also owned by the Museum.