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In this study, to evaluate the effect of isolates of different species of Trichoderma on some morphological traits of canola and to obtain suitable antagonist isolates for biological control of canola crown rot disease, the effect of 71 Trichoderma isolates on Sclerotinia sclerotiorum was investigated in the laboratory by volatile compound and non-volatile metabolite methods. In the volatile metabolite assay, the isolate ARCTr281 (T. harzianum) was more efficient than the other isolates with a 20% reduction in hyphae density and non-formation of S. sclerotiorum sclerotia. In the non-volatile metabolite assay, ARCTr272 (T. harzianum) with 73.7 and 62.22 at 25 and 15% concentrations and T. viride isolate ARCTr432 (20.37%) at 5% concentration were successful in inhibiting S. sclerotiorum mycelia growth. Six superior isolates were selected for greenhouse studies. Using two-stage Trichoderma isolates in the greenhouse, height, fresh and dry weight of shoots and roots, number of pods, pod length, pod diameter and number of seeds per pod in the presence of pathogen all increased. The results of principal component analysis showed that the first two components accounted for 86% of the total variation among the data. The results showed that for the first component, the traits of total grain weight, pod diameter, branch number, shoot dry weight and fresh weight of root were the most important traits in grouping the isolates. In the trait second component, plant height and number of seeds per pod were important traits. Mean comparisons were performed using an LSD test and showed significant differences between the fungi used in non-volatile metabolite and greenhouse studies. According to the results of this research, the fungal isolates of T. harzianum (ARCTr281, ARCTr272 and ARCTr418) were the most effective antagonists in improving plant traits and controlling canola rot disease in both the laboratory and the greenhouse.