With the improper application of fungicides, begins to develop resistance to fungicides, and biological control is one of the potential ways to control it. We screened two strains of ; JDF3 and RSS-1, which had an efficient inhibitory effect on They could inhibit mycelial growth, the germination of the cysts, and the swimming of the motile zoospores. To elucidate the response of under the stress of and , and the molecular mechanism of biological control, comparative transcriptome analysis was applied. Transcriptome analysis revealed that the expression gene of showed significant changes, and a total of 1616 differentially expressed genes (DEGs) were detected. They participated in two major types of regulation, namely "specificity" regulation and "common" regulation. They might inhibit the growth of mainly by inhibiting the activity of ribosome. A pot experiment indicated that and enhanced the resistance of soybean to , and their control effects of them were 70.7% and 65.5%, respectively. In addition, fermentation broth could induce an active oxygen burst, NO production, callose deposition, and lignification. could also stimulate the systemic to develop the resistance of soybean by lignification, and phytoalexin.