In 1973 the IZW's predecessor, the Research Station for Vertebrate Research (FWF) was formed under the auspices of the Academy of Sciences of the GDR. The FWF was under the direction of Prof. H. Dathe (who simultaneously ran the Tierpark Berlin) until 1990, and of Prof. R. Ippen until 1992. Research at the FWF focused on questions about the health status and biology of vertebrates, on developmental biology and parasitology of lifestock, and the diagnosis of necropsies of wildlife from the Tierpark Berlin and other zoos.

After unification, the German Science Council evaluated all research institutes of the former Academy of Sciences of the GDR in 1991. It recommended that the work of the FWF be continued by creating a new institute for wildlife research with a different legal status, a modified misson and an expanded scope and purpose. The German Science Council recommended to assign the institute legal status as a national research institute jointly funded by the federal government and the state of Berlin. The IZW thus first joined the group of national institutes labelled the "Blaue Liste" and then its successor organisation, the Leibniz community of scientific institutes, since 2002 Leibniz Association.

In March 1992, Prof. Dr. Reinhold R. Hofmann was appointed as founding director of the IZW; he retired at the end of 1999. Based on a cooperation agreement between the IZW and the Free University of Berlin, the director of the IZW also holds a full professorship for interdisciplinary zoo and wildlife science at the Faculty of Veterinary Medicine of the Free University Berlin.

The IZW and seven further scientific research institutes in Berlin, all successors to institutes of the former Academy of Sciences of the GDR, then formed an administrative unit called the Forschungsverbund Berlin e.V. The Forschungsverbund represents and coordinates the common interests of all member institutions and comprises a central unit that provides key administrative services.

The German Science Council evaluated the IZW again in 1998, to assess the changes at the IZW over six years from its roots in the FWF to a modern wildlife research institute, and to assess its perspectives for future development. This evaluation was very positive and a strong endorsement of the enormous efforts of the IZW and its founding director to develop a modern wildlife research institute firmly based on an evolutionary approach.

Since 2000 the IZW’s director is Prof. Dr. Heribert Hofer.