Background : Korean ginseng is an important cash crop in Asian countries. However, plant yield is reduced by pathogens. Among the Ilyonectria radicicola-species complex, I. mors-panacis is responsible for root-rot and replant failure of ginseng in Asia. It is essential to find a way to reveal the existence of the pathogen before starting cultivation. Therefore, qRT-PCR method is developed to detect and quantify the pathogen in ginseng soils. Methods and Results : In this study, species specific Histone H3 primer set is developed for the quantification of I. mors-panacis. The primer set was applied on DNA of other microbes to evaluate its sensitivity and selectivity on I. mors-panacis DNA. Sterilized soil samples artificially infected by the pathogen in different concentrations were used to evaluate the ability of the primer set to detect the pathogen population in the soil DNA. Finally, the pathogen was quantified in many natural soil samples. The designed primer set was found to be sensitive and selective to I. mors-panacis DNA. In artificially infected sterilized soil samples, the estimated template using qRT-PCR was positively correlated with the pathogen concentration in soil samples (R2=0.94), disease severity index (R2=0.99), and colony forming unit (R2=0.87). In the natural soils, the pathogen was recorded in the most of fields produce bad yields with the range of 5.82 ± 2.35 to 892.34 ± 103.70 pg/g of soil. Conclusion : According to the presented results, the proposed primer set is applicable for estimating soils quality before ginseng cultivation. This will help in the disease management and crop protection in the future.