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The Department of Plant Breeding of the Polish Academy of Sciences was created in 1954, on the inititiative of Professor Stefan Barbacki. The establishment of the Department was the implementation of his idea to create a strong agricultural science center in the Wielkopolska Region.

On January 1, 1961 the Institute came into being as the Department of Plant Genetics of the Polish Academy of Sciences, as a result of the unification of the Department of Plant Breeding PAS in Poznan and the Department of Genetics PAS in Skierniewice.

In January 1979 the Department was converted into the Institute of Plant Genetics of the Polish Academy of Sciences with the aim to perform genetic studies on crops.

In January 2013, the Institute changed its organisational research structure - 5 Departments divided into 16 Research Teams replaced existing 10 Laboratories.