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Continuous monocropping can cause the buildup of autotoxins (e.g., phenolic compounds) in the soil, which can alter soil microbial community and inhibit plant growth. However, how different phenolic compounds affect certain soil microbiota is unclear. Here, we studied the response of cucumber rhizosphere Trichoderma spp. community to exogenously applied ferulic and p-coumaric acids by polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) and real-time PCR techniques. Results showed that ferulic acid, but not p-coumaric acid, increased the Trichoderma spp. abundance, and this increase were positively correlated with ferulic acid concentration. Moreover, ferulic acid changed the community structure, increased the number of DGGE bands, Shannon wiener, and evenness index values, while p-coumaric acid had no effect on all these parameters of Trichoderma spp. community. These results suggest that these two phenolic acids affected Trichoderma spp. differentially at the community level.