In 1912 Schmalhausen became a professor of zoology in Kyiv University. From 1920–1930 he was head of the Department of Vertebrate Zoology. During 1930–1941 Schmalhausen was director of Institute of Zoology in Kyiv, at the same during 1936–1948 he was director of Institute of Evolutionary Morphology in Moscow and during 1939–1948 - also a head to the Department of Darwinism in Moscow University. The Institute of Zoology in Kyiv was later named in his honour the I. I. Schmalhausen Institute of Zoology.