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Background Fungal endophytes produce many secondary metabolites that can reduce root rot diseases. Soybean is a particularly important crop worldwide. Endophytic fungi can be isolated, identified, and incorporated into sustainable agriculture for the biological control of many diseases. Results The aim of this study was to isolate some endophytic fungi for controlling the most important diseases of soybean plants and to study the mechanisms underlying this biocontrol regarding the suppression of pathogens. Ten endophytic fungi were isolated from soybean plants. Among them, the 3 fungi isolates that exhibited a high percentage of antagonistic activity against Rhizoctonia solani, the causal pathogen of root rot disease of soybean plants, were identified as Trichoderma longibrachiatum S12, T. asperellum S11, and T. atroviride PHYTAT7. The 3 fungi isolates had the ability to produce pectinase and chitinase and to solubilize phosphors. Moreover, they produced siderophores and indole acetic acid (IAA), which have a strong effect on the growth of the plants. The 3 isolates reduced disease severity by 64, 60, and 55%, respectively than the infected control. Conclusion The results suggest that certain endophytic fungi associated with soybean plants have potential for the management of root rot diseases in soybean. Moreover, these isolates can be considered as having a growth-promoting effect in soybean plants.