The ancestor of today´s Department of Plant Physiology is The Institute of Plant Anatomy and Physiology, established in 1901 by Ass. Prof. PhDr. Bohumil Němec (1866-1966). Nevertheless, plant anatomy and physiology as a new natural scientific branch was introduced earlier, in 1899, by the conferment of Bohumil Němec mentioned above. That time, Němec was 26 years old. He was the first to find and describe the statolite starch as a sense of gravity of Earth (1900). He was also interested in karyology, regeneration, excitability, physiology of fertilization and mineral nutrition. After his Especial Professor designation (1903) and following Professor of plant anatomy and physiology designation (1907) he became a deacon of Philosophical Faculty in 1919. Being a deacon (1919-1920) he triggered the division of Philosophical Faculty and in 1921-1922 he even held a rector position at Charles University.

 An important part of his scientific work are textbooks, monographs and handbooks. His Botanical Microscopic Methods is still used in many laboratories. He was an important popularizer of Plant Science and Biology as well (The Soul of Plants, 1937, The Green Kingdom, 1939, The Life of the Plants, 1941). He was in the lead of the department till 1939, when he was followed by Prof. PhDr. Silvestr Prát, DrSc. Prof. Prát introduced modern physical-chemical methods at the institute. In the 20s, he did physiological radioizotopic experiments and later he used radioactive carbon (14C) for the monitoring of plant humus solution intake. At the institute, he founded an unique collection of cyanobacterial, algal and hepatics (Marchantiophyta) pure cultures. He possessed substantial pedagogical abilities that were proved also in his textbooks (The Chemical and Physical-Chemical Physiology, 1932) and handbooks (The Plant under the Microscope, 1934).

 After university institutes´ cancellation in 1950 and two years´ administrative phusion of all university workplaces, the department of plant physiology, microbiology and genetics was established in 1952. Later, a new soil microbiology section was added. Till 1954 and later in the years 1960-1964, Professor Prát was the head of the department, meanwhile he was shifted with Professor RNDr. Jaromír Seifert, DrSc. (1954-1960, 1964-1980). In the period of Prof. Seifert activity, an independent department of plant physiology and soil biology was established in 1959, however, after his retirement, the soil biology section perished. In 1980, Profesor RNDr. Lubomír Nátr., DrSc. became the head of the department. With his attitude, broad insight in the plant physiology issue and pedagogical abilities, he captivated and attracted many students to the subject. In the position of the head of the department, in 1990-1991 he was followed by Prof. RNDr. Jaroslav Pazourek, CSc. In 1992-1997 was in the lead Ass. Prof. RNDr. Jiří Luštinec, CSc. and in 1997-2003 Prof. RNDr. Zdeněk Opatrný, CSc. Finally, the lead was taken over by a woman, in 2003, it was Ass. Prof. RNDr. Libuše Pavlová, CSc. who won huge approval by many students for her patience, treatment and extraordinary pedagogical abilities. In 2006, Ass. Prof. Jana Albrechtová, Dr. was elected as a following leader of the department and till today, she has been in her office.