Before the German and the Czech part of Charles University were separated, botany was taught at the Medical Faculty and other life sciences were taught at the Philosophical Faculty. In 1775 „Institutiones Philosopicae“ by prof. K. Sanger were issued. In his work, Sanger included general botany with comments on physiology. Yet, an independent Department of Botany at the Philosophical faculty was not established till 1849. The professor at the department became V. F. Kosteletzky. In 1858 and 1859 taught here Julius Sachs who became later famous later for his discoveries in the plant physiology. An independent Department of Plant Anatomy and Physiology was established in 1871 when G. A. Weisse was the chair. In 1882, the university was separated into two parts: the Czech and the German one. At the Philosophical Faculty, the professor of the Department of Botany was L. J. Čelakovský. After many years of complicated events including university separation an constant moving of the botanical institute, the new buildings in Benátská and Viničná street were built. The building in Viničná street was a part of the German university, whereas the building of the institute of botany in Benátská street belonged to the Czech side. In 1898, an assistant of professor Čelakovský, Bohumil Němec, was appointed to establish the Institute of Plant Anatomy and Physiology. After his habilitation in 1899, B. Němec became the Chair of the new institute. In 1907 he became a professor and continued in his research – his major contribution is the statolite theory that keeps being cited till now.
Shortly after the declaration of independence of the Czech Republic, B. Němec pushed through the separation of the Philosophical Faculty and the Faculty of Life Sciences. In his function, he was later, in 1938, substituted by his colleague, professor Silvestr Prát. Another professor that time was J. Kořínek. After the liberation in 1945, the former German botanical institutes located in Viničná street joined the Czech part. In 1950 the common Department of Botany was established, however in 1952 the huge institute was divided into the Department of Botany (in Benátská street) and Department of Plant Physiology, Microbiology and Genetics (Viničná 5) with S. Prát as the Chair. According to the mutual agreement at the institute, the section of plant cell biology and anatomy was established in 1953. In 1959 a huge reorganization resulted in separation of the Department of Microbiology and Genetics. On the other hand, the soil microbiology section was amended to the newly established Department of Plant Physiology and Soil Microbiology. Among the chairs of the Department were many important personalities, such as prof. J. Seifert, prof. L. Nátr, prof. J. Pazourek, assoc. prof. J. Luštinec, prof. Z. Opatrný, assoc. prof. L. Pavlová and prof. J. Albrechtová. Currently, the chair of the Department is Dr. Lukáš Fischer.
The history and establishment of our department is described in a handwritten manuscript by Stanislav Lhotský from June 6, 1976.