Institute of Plant Physiology and Genetics is one of the oldest biological Institutes of the Bulgarian Academy of Sciences. It was founded in 1948 by Academician Metodii Popov, as 'Institute of Biology'. In the subsequent year it was merged with the Institute of Applied Biology and Organism Development. In the new formed Institute named 'Institute of Biology', three departments existed: Biology, Agrobiology and Forest Biology. In 1953 and 1954 from the Departments of Agrobiology and Forest Biology two independent Institutes were founded - Institute of Plant-Growing and Institute of Forestry. The Department of Biology, headed by Acad. M. Popov, was then expanded to form five laboratories: Stimulation, Biology, Immunology, Cytology, and Helminthology. From the Laboratory of Helminthology originated the Central Laboratory of Helminthology (1954) and from the Laboratory of Cytology - the Institute of Molecular Biology (1960).
After the death of Acad. M. Popov (April 19, 1954), the Institute was renamed to 'Acad. M. Popov Institute of Biology'. From 1954 to 1958 it was headed by Professor P. Iliev, and from 1958 to 1970 by Professor K. Popov. Since 1960 the scientific investigation of the Institute have been directed to plant organisms only, and two main Departments were founded - Stimulation and Inhibition, and Plant Physiology and Biochemistry.
In 1964 the Institute was renamed to 'Acad. M. Popov Institute of Plant Physiology', which is its present name. Five departments were specialized: Plant Stimulation and Inhibition, Plant Physiology, Plant Biochemistry, Plant Cytogenetics, and Plant Biophisics. From the last one, the Institute of Biophysics was originated. During the period 1965-1973 the structure of the Institute was reorganised on the principle of problem groups: Stimulation and Inhibition (with three Laboratories), and Photosynthesis (with three Laboratories). In 1973, the Department of Plant Physiology from the Institute of Plant Growing was joined to the Institute of Plant Physiology, and three Departments were organised: Plant Growth and Development (with three Problem Groups); Mineral Nutrition (with two Problem Groups) and Photosinthesis (with two Problem Groups).
The next change in the organisational structure of the Institute was made in 1976 - five Departments were founded: Plant Growth and Development (with Laboratory on Frost Resistance), Physiology and Ecology of Photosynthesis, Biochemistry of Photosynthesis, Mineral Nutrition and Water Relation, Plant Selfregulation (with Laboratory on Seed Physiology and Biochemistry). In 1978, two Laboratories (Frost Resistance and Seed Physiology and Biochemistry) were separated as independent scientifiec units in the Institute. In 1983 a Laboratory of Chemical Phytoeffectors set up from the Department of Plant Growth and Development. Three years later the Institute adopted the Department of Algology.
From 1971 to 1989 the Institute was headed by Prof. T. Kudrev, Corresponding Member of the Bulgarian Academy of Sciences.
From 1989 to 2005 Director of the Institute was Acad. Emanuil Karanov. During his leadership the current structure of the Institute was formed: Department of Algology, Department of Genomics and proteomics, Department of Mineral nutrition and water relations, Department of Photosynthesis, Department of Regulation of plant growth and development, and Laboratory of Plant stress molecular biology.
After the death of Acad. Emanuil Karanov, the Institute is leaded by its current director Prof. Lozanka Popova.
The above mentioned modifications in the organisation of the Institute express also the changes in the priority of the scientific problems. Undoubtedly, as a principal problem in the Institute's history endured the established by Acad. M. Popov and developed as a tradition hypothesis of the plant stimulation and inhibition, or regulation of plant growth and development.