The existence of a complex relationship between soil microbes and ginsenoside contents in their host plants has been reported by previous studies. Here, we analyzed the interaction between the root pathogens and the ginsenoside content in the roots of American ginseng. Two fungal pathogen species were isolated from diseased American ginseng roots, and identified as Fusarium oxysporum (isolate C1) and Fusarium solani (isolate F19) by molecular sequencing analysis. To determine the effect of Fusarium-mediated infection of American ginseng roots, the contents of three ginsenosides, ginsenosides Rb 1 , ginsenosides Re and ginsenosides Rg 1 , were monitored over a time course of 120 h post infection using high performance liquid chromatography (HPLC). We found that the level of Rb 1 was rapidly upregulated upon fungal infection, whereas the contents of Re or Rg 1 were not altered significantly. Furthermore, the presence of Rb 1 , but not Re or Rg 1 , significantly inhibited conidium germination of both Fusarium species. Thus, Rb 1 is likely the disease-resistance compound produced by American ginseng roots in response to the pathogenic fungi. Our study is the first to report the three ginsenosides with different chemical structure respond differently to soilborne pathogen infection.