The soybean breeding work at the Agricultural Institute Osijek has focused on the permanently development of high-yielding cultivars with genetic yield potential of 5-6 t/ha, satisfactory grain quality (protein and oil content), high tolerance to the principal diseases (Peronospora manshurica, Sclerotinia sclerotiorum, Diaporthe/Phomopsis complex), high resistance to lodging, stress conditions over vegetation and pod shattering as well as satisfactory stability in level and quality of grain and wide adaptability. Results of this continued and intensive breeding work are 36 registered cultivars which significantly contributed and contribute to the development, improving and increasing of soybean production in Republic of Croatia. Further genetic improvement of soybean cultivars is based on the modern breeding strategies including combination of conventional breeding methods and recent chemical, biochemical, phytopathology and molecular analyses. Regarding to molecular analyses, in recent years, in the frame of the soybean breeding program has initiated by application of molecular markers technology as criterion for estimation genetic diversity for both soybean germplasm and pathogens from Diaporthe/Phomopsis complex on soybean, as well. The initial fingerprinting of several OS soybean genotypes has performed in collaboration with the University of Guelph (Canada) in their biomolecular laboratory using simple sequence repeats (SSR). The obtained results enabled new access in choosing parental pairs. Combining molecular markers technique with pedigree information, phenotypic markers and statistical procedure has provided a useful tool for more accurate and complete evaluation of genetic diversity and its more effective utilization into current soybean breeding program. The detection of pathogens from Diaporthe/Phomopsis complex on soybean on molecular level has performed in collaboration with the Istituto Sperimentale per la Patologia Vegetale (Rome, Italy) in their mycological and biomolecular laboratories using method of artificial infection and RFLP markers. Obtained data are incorporated in our breeding work for improving soybean genotypes tolerance on mentioned pathogens. In a whole, implementation of molecular marker technology into soybean breeding program at the Institute represents basis for significantly increasing of its quality, success, efficiency and competitiveness and enables further genetic improvement of cultivars. Each increasing of soybean production, resulting from genetic improved cultivars, is considerable national economical profit.