With biological simulation experiment and chemical analysis, this paper studied the allelopathy of carbohydrates, amino acids and organic acids in the root exudates from two genotypes soybeans (9536 and Jilin 30) on the pathogenic fungi of root rot. The results showed that the water soluble carbohydrates in the root exudates from test soybeans significantly promoted the growth of Fusarium oxysporium and Fusarium semitectum at low concentrations and inhibited their growth at high concentrations, but had no evident influence on Gliocladium roseum. The water soluble amino acids from the root exudates demonstrated different actions, i. e., at middle and high concentrations, those from 9536 significantly inhibited the growth of Fusarium oxysporium, Fusarium semitectum and Gliocladium roseum, while those from Jilin 30 mostly promoted their growth. The organic acids from the root exudates of 9536 and Jilin 30 significantly inhibited the growth of Fusarium oxysporium, Fusarium semitectum and Gliocladium roseum. It's suggested that there existed interactions between the root exudates of the two genotypes soybeans and the pathogenic fungi of root rot. Different genotypes of soybean may have different allelopathy on pathogenic fungi of root rot.