In this biocontrol research, we evaluated disease suppressive effects of antagonistic bacterial strains ISE13 and KJ1R5 against Korean ginseng root rot caused by P. cactorum. We also examined the effects of nutrient solution in the hydroponic culture system for Korean ginseng on biological activity of the bacterial strains. As results of dual culture tests of the bacterial strains on V8 juice agar, the strain ISE13 showed antifungal activity against P. cactorum and other plant pathogenic fungi, but the strain KJ1R5 did not. When their inhibitory effects against infection of P. cactorum on the roots grown in either nutrient solution or water were tested, the strains ISE13 and KJ1R5 inhibited the disease severity of Korean ginseng roots only grown with water, compared to buffer-treated, inoculated controls. However, the nutrient solution used for hydroponic cultures of ginseng in pots caused higher levels of disease severity by the strains ISE13 and KJ1R5 from 18.8% to 40.0% and from 24.3% to 45.0%, respectively. In this study, the bacterial strains ISE13 and KJ1R5 could be potentially biocontrol agents to suppress Korean ginseng root rot caused by P. cactorum. However, more attention using nutrient solution in hydroponic cultures for Korean ginseng production should be applied in biocontrol of plant diseases using the antagonistic microorganisms.