In 1954, on the initiative of Professor Stefan Barbacki, the Department of Plant Breeding of the Polish Academy of Sciences was established, by Resolution No. 187/54 of the Scientific Secretariat of the Presidium of the Polish Academy of Sciences of December 21, 1954. The establishment of the Department was the implementation of Professor Barbacki's idea of creating a strong center of agricultural sciences in Wielkopolska. The resulting Department had no seat and was located in various rooms, mainly belonging to the Higher School of Agriculture. Six years later, on January 1, 1961, the Department of Plant Breeding of the Polish Academy of Sciences was merged with the Department of Genetics of the Polish Academy of Sciences in Skierniewice, which had been in existence since 1952, and was headed by Professor Edmund Malinowski. The Department of Plant Genetics of the Polish Academy of Sciences, based in Poznań, established as a result of the merger, was to be, according to Professor Barbacki's intention, a center for genetic research on cultivated plants. The department in Skierniewice, headed by Professor Malinowski, operated as a branch - Genetic Research Centre.

In the 1950s and 1960s, there were six laboratories within the Department of Plant Breeding of the Polish Academy of Sciences, headed by eminent scientists from the Poznań community. The Laboratory of Genetics and Plant Breeding was headed by prof. Stefan Barbacki, Laboratory of Plant Physiology - by prof. Jerzy Czosnowski, Laboratory of Cytogenetics - by prof. Teresa Hulewiczowa, Laboratory of Plant Biochemistry - by prof. Jerzy Pawełkiewicz, Laboratory of Mathematical Statistics - by prof. Regina Elandt, Laboratory of Phytopathology - by prof. Wladyslaw Błaszczak.

The branch Genetic Research Center in Skierniewice had the following laboratories: Cytogenetics (later Analytical Genetics), Plant Genetics, Fungi Genetics, and the Laboratory of Genetic Resources of Cultivated Plants, established in 1970. (The Laboratory of Genetic Resources of Cultivated Plants was transformed in 1974 into the Botanical Garden of the Polish Academy of Sciences, currently the Polish Academy of Sciences Botanical Garden - Center for the Preservation of Biological Diversity in Powsin).

The scientific profile of the Department of Plant Genetics of the Polish Academy of Sciences was, on the one hand, related to the genetics of crop plants and related fields, such as cytology, physiology and biochemistry, and on the other hand, breeding, experimentation and biometrics, especially of cereals and fodder plants. The research topics of the Department focused mainly on issues related to the polyploidization of crop plants, inter-varietal and inter-specific crossing, and plant resistance to diseases.

In 1970, the Plant Genetics Department of the Polish Academy of Sciences gained its current premises at Strzeszyńska Street in Poznań. At that time, new laboratories were established, and the existing research teams were strengthened in terms of staff.

Since the early 1970s, new research in quantitative genetics has been initiated, including the issues of heterosis and transgression effects, as well as studies in population genetics. During this period, an innovative research topic related to in vitro cultures was also undertaken. The research issues carried out in this area were related to the analysis of tissue and cell differentiation processes, methods of obtaining haploids and lines of doubled haploids through androgenesis and gynogenesis, and the elimination of chromosomes in cereals, grasses and legumes. In vitro methods were used to obtain distant hybrids by cultures of immature embryos obtained from intergeneric crossings. Research on induced mutations of plants to extend the variability of crop plants using physical and chemical mutagenic agents was also innovative. The research topics included the aspects of mutation formation and increasing their frequency, as well as the acquisition of mutants for genetic analysis and practical cultivation of crop plants.

In the 1970s, many scientists started their scientific careers in the Department of Plant Genetics of the Polish Academy of Sciences, then working in other research centers in the country and abroad, including professors: Andrzej Guranowski (University of Life Sciences in Poznań), Maria Guranowska and Henryk Popiszny (Institute of Plant Protection - State Research Institute in Poznań), Adam Łukaszewski (University of California in Riverside, USA), Stefan Malepszy and Zbigniew Przybecki (Warsaw University of Life Sciences), Jolanta Małuszyńska and Mirosław Małuszyński (University of Silesia), Jerzy Puchalski and Jan J. Rybczyński (Polish Academy of Sciences Botanical Garden - Center for the Preservation of Biological Diversity in Powsin).

On January 30, 1979, the Presidium of the Polish Academy of Sciences, by resolution No. 1/79, established the Institute of Plant Genetics of the Polish Academy of Sciences, specifying at the same time that the subject of its activity is scientific research in the field of plant genetics, with particular emphasis on the needs of agriculture.

As a consequence of the development of new research methods in the field of genetics and molecular biology in the 1990s, there were also changes in the research area of the Institute. New research methods and available modern equipment allowed for the analysis of plant genomes at the level of DNA structure, the creation of genetic and physical maps of genomes, the identification of genes responsible for the expression of important traits and the study of their functions, as well as the creation of new biotechnological methods useful in breeding practice. In the following years, along with the emergence of new directions in genetic research, the laboratories of the Institute also changed, both in terms of the research subject, as well as the composition and name (see section in Polish).