Wheat powdery mildew (WPM) is one of the most devasting diseases that affects wheat yield worldwide. Few efforts have been done to control such a serious disease. Looking for an effective way to control WPM is urgently needed. Biological control is an effective way in controlling plant diseases worldwide. In this study, the efficiency of three different Trichoderma spp. in controlling WPM at seedling growth stage was tested using 35 highly diverse wheat genotypes. Highly significant differences were found in WPM resistance among the four treatments confirming the efficiency of Trichoderma in controlling WPM. Out of the three species, Trichoderma asperellum T34 (T34) was the most effective species in controlling WPM as it reduced the symptoms with a percentage of 50.56%. A set of 196 wheat genotypes was used to identify the genetic control of the WPM induced resistance by T34. A total of 39, 27, and 18 gene models were identified to contain the significant markers under Pm, T34, and the improvement in powdery mildew resistance due to T34 (T34_improvement) conditions. Furthermore, no gene model was common between T34 and Pm suggesting the presence of completely different genetic systems controlling the resistance under T34 and Pm. The functional annotation and biological process pathways of the detected gene models confirm their association with the normal and induced resistance. This study, for the first time, confirm the efficiency of T34 in controlling WPM and provide a deep understanding of the genetic control of induced and normal resistance to WPM.