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The Institute was founded in 1934 on the basis of the Laboratory of Evolutionary Morphology, founded by the famous Russian scientist Academician Alexei Nikolaevich Severtsov, who was the first director. In 1936 the Institute was divided in two: the Paleontological Institute and the A.N. Severtsov Institute of Evolutionary Morphology (IEM).

After a series of transformations and renaming in 1967, the Institute was named the A.N. Severtsov Institute of Evolutionary Morphology and Ecology of Animals (IEMEA). In 1994, due to the concentration of fundamental research on the problems of ecology, evolution and biodiversity, the Institute was renamed and received its current name. The formation of the Institute in its modern form is associated with the name of Academician Vladimir Evgenievich Sokolov, who was the director of the Institute in 1967 - 1998. Thanks to his activities, the Institute has become one of the leading biological research institutions in Russia.

In 1998, the Institute’s head researcher was Academician Dmitry Sergeevich Pavlov, a leading expert in the field of behavior of lower vertebrates, full member of the Russian Academy of Sciences (1992), foreign member of the Lithuanian Academy of Sciences (2004), visiting professor at the University of Montana (2002), laureate of the State Prize of the Russian Federation 2012.

Now the director of the institute is Academician of the Russian Academy of Sciences Rozhnov Vyacheslav Vladimirovich. Specialist in behavioral ecology of mammals and biodiversity. He developed a number of new approaches and concepts, non-invasive and remote research methods, methods of satellite telemetry and molecular diagnostics in behavioral ecology. Under his leadership and with his participation, unique material was collected on the biology of large predators and marine mammals - tiger, leopard, snow leopard, polar bear, beluga whale, gray whale.

The Institute studies the problems of general and specific ecology of animals, biodiversity, behavior and evolutionary morphology of animals, and develops recommendations for nature protection.