Johannes Theodor Schmalhausen (1849–1894) was a Russian botanist of German descent, known for his studies of East-European plants.

After attending the Gymnasium, Schmalhausen studied botany at the University of St. Petersburg graduating with a magister degree in 1874.

He was awarded the Gold Medal of the University for the botanical essay "On plant hybrids.

He studied in Strasbourg (with Heinrich Anton de Bary and Andreas Franz Wilhelm Schimper), Zurich (with Oswald Heer), Vienna, Prague, Munich, Berlin, visited the Alps, Northern Italy and Southern France.

In 1877 he became a conservator at the herbarium of the Imperial Botanical Garden in Saint Petersburg and was ordained as a professor (Russian doctorate).