Rhizoctonia rot disease is one of the most important diseases of crop plants and has a worldwide distribution. Despite the relative effects of certain chemicals to control the disease, it seems that biological control is one of the appropriate methods of control. Beauveria bassiana is an endophytic fungus that can colonize a wide range of plants in a systemic manner and enhance plant resistance. In this study the ability of three strains of B. bassiana fungus for control of cotton damping- off were investigated. Results showed that the isolates used, in addition to their endophytic activities, can significantly reduce the disease severity in plants. Based on the result of greenhouse studies and measurement of peroxidase activity and total plant protein, the KJ24 isolate at a concentration of 10⁷ spores/ml was found to be the most suitable treatment to control the disease. It appears that this ability is due to the stimulation of plant growth. Moreover, concentrations of 10⁷ spores/ml of isolates TS7 and TS12, were also able to significantly reduce the severity of the disease. Based on the observed increase of total protein in plants treated with these isolates, the reduction of disease could be due to the induction of plant resistance by these isolates.