The Museum für Naturkunde is an independent trust under public law governed by:
• Stiftungsrat (Board of Trustees)
• the appointed Director General, the Head of the Museum
• wissenschaftlicher Beirat (Scientific Advisory Board)

The museum is divided into the following Departments:
• The Department for Collections
• The Department for Research Infrastructure
• The Department for Exhibitions and Public Education
• Directorate General, including Administration

Research is organised in temporary Science Programs ("Forschungsbereiche"), which currently include the following:
• Discovery of Biodiversity
• Genome - Organism - Environment
• Diversity Dynamics
• Impact, Meteorites and Geological Processes
• Collection Development
• Science Communication and History of Science

The number of Science Programs and topics are flexible and depend on the academic focus of the Museum at any given time. Each Science Program has its own spokesperson.

Further information can be found in the organisation chart of the Museum.