Plants are associated with a wide range of microorganisms, and these interactions induce changes in both the plant and microorganism. Transcription factors play an important role in the regulation of large numbers of genes associated to plant–microbe response. WRKY transcription factors have been involved in the responses to plant–pathogen interactions, but little is known about WRKY transcription factors in beneficial plant–microbe interactions. In this study, the expression patterns of Arabidopsis thaliana WRKY genes were evaluated during the interaction with the beneficial fungus Trichoderma atroviride. Eight WRKY genes, AtWRKY8, AtWRKY33, AtWRKY38, AtWRKY42, AtWRKY54, AtWRKY57, AtWRKY60 and AtWRKY70, were analyzed by quantitative RT-PCR. These WRKY genes were found differentially expressed in a time-dependent manner during T. atroviride interaction. Our data suggest that T. atroviride induces the expression of positive regulators in jasmonic acid-mediated pathway such as AtWRKY8, AtWRKY33, AtWRKY38, AtWRKY42 and AtWRKY60, while salicylic acid pathway regulated by AtWRKY70 and AtWRKY54, could be activated at later stages of the interaction, when the fungus is fully established in the plant roots. In addition, Trichoderma treatment regulates the expression of WRKY genes such as AtWRKY57, AtWRKY60 and AtWRKY33 related to response to abiotic stresses. In this sense, WRKY transcription factors regulation suggests a complex signaling network in this beneficial plant–microbe interaction.