Five isolates of Trichoderma spp. were investigated, in a preliminary study, for their efficiency in controlling Rhizoctonia root rot of pepper (Capsicum annuum L.). GC-MS analysis of most active Trichoderma spp. extracted secondary metabolites were studied. The major compounds identified by GC-MS analysis included hexadecanol, nonadecene, 1,2-benzenedicarboxylic acid, octadecenoic acid (z) and hexadecanol, 2-methyl. These compounds have been found to play an important role in controlling plant diseases. The results of antagonistic activity of three isolates proved higher efficiency in controlling R. solani. Browning of the R. solani mycelium was observed where mycoparasitism occurred. The parasitism of R. solani hyphal cells by Trichoderma harzianum was studied by light and scanning electron microscopy. Sequence data of R. solani isolates (R.1, R.2 and R.4) have been submitted to the GenBank under accession numbers (MZ267232, MZ267234 and MZ267689), respectively. The most effective isolates i.e., T. asperellum, T. hamatum and T. harzianum in addition to their mixture were formulated in different forms i.e., suspension and powder, then tested at different concentrations under the greenhouse and protected cultivation conditions. Results of greenhouse studies indicated that all isolates and their mixture were effective in controlling pepper root rot disease and increasing percentage of survived plants. Moreover, results showed that suspension was effective than powder in reducing the disease. Higher bio-control efficiency at protected cultivation was obtained when the mixture of isolates was used at high concentration. Most of the Trichoderma spp. studied in the present work have been able to reduce severity of R. solani.