Abstract: In order to obtain biological function bacteria which could enhance the control stability of plant fungal diseases, twelve strongly antagonistic endophytic bacteria were isolated from soybean and corn roots by the method of confrontation plating cultivation. All strains had antagonistic activity against crop pathogens Rhizoctonia solani, Fusarium oxysporum f. sp. glycine and Fusarium oxgsporum f. sp. lycopersici. Based on 16S rRNA gene sequence analysis, the twelve isolates were closely related to Bacillus, Paenibacillus and Pseudomonas. Five isolates were chosen for pot experiment, and the results showed that these isolates were beneficial for controlling soybean root rot disease. Among them, strains J1 and J2 had a good control effect of 20.4% and 32.1%, respectively.