It was established in 1955 at the Agricultural Institute under the name Department for Industrial and Forage Plants. The purpose was to advance the main industrial and forage cultures in eastern Croatia, and most of the activities were related to agricultural engineering research. During the initial period, the Department was headed by Marko Budišić, BSc. In the early 1960s the Department was divided into the Department for Industrial Plants and Seed Production and Processing and the Department for Forage Plants and Seed Production and Processing.

From 1967 to 2009, the Department was headed by Marija Vratarić, PhD, who enhanced the personnel capacities of the Department and since 1993 it is called the Department of Industrial Plant Breeding and Genetics. The breeding programmes on soybean, sunflower, and winter rapeseed have been developing further, and the programmes regarding less significant cultures (flax, hemp, castor, and others) were abandoned. The breeding work in the department, which intensified significantly in the last 40 or so years, resulted in the creation and recognition of our own cultivars and hybrids. Their commercialisation through seed production and processing created the basis for a more quality scientific and research work.

Since 2010 the Department has been headed by Aleksandra Sudarić, PhD. The main goal of breeding is to continuously create new better genotypes of soybean and sunflower for the production practice, by using the appropriate breeding methods, while implementing constant monitoring and using the trends used in the world for breeding these cultures. Aside from the breeding work, the Department also conducts various agricultural engineering research studies on their own product range in order to be able to provide recommendations in wider practice.

In the breeding work so far, in the period from 1976 to 2016, the Institute received recognition for 43 soybean cultivars (3 in the Republic of Hungary) within the 00-II maturity group and 13 sunflower hybrids (2 in Slovakia and 2 in Bosnia and Herzegovina).

The recognised soybean cultivars are being planted on large areas for wide production (about 10 cultivars from the Institute are now being planted on about 70% of the all the soybean planting surfaces in the Republic of Croatia) and they are contributing significantly to the increase and advancement in production.

The scientists from the Department have published over 250 scientific and professional papers, including master and doctoral papers, seven books, several studies, and edited 11 Proceedings from the soybean conferences in Osijek. Over 100 papers are indexed in reference databases. Research results are being shown at national and international symposiums and during direct communication with the manufacturers. In the preceding period, some of the scientists from the Department received significant scientific and professional recognitions for their work.