In the present study, the capacity of three native tomato-associated rhizobacteria (Bacillus subtilis B2, B. thuringiensis B10, and Enterobacter cloacae B16) to suppress Sclerotinia Stem Rot in tomato and to improve growth was investigated in two tomato cultivars. The three bacterial strains were tested against S. sclerotiorum either singly or as consortium and their efficacy was compared to a fungicide control. All bacteria-based treatments were found to be more effective in suppressing disease than chemical fungicide on both cultivars and in both year trials. The disease-suppression and growth-promoting abilities of the treatments tested varied significantly depending on bacterial strains used, tomato cultivars grown, and year trial. Overall, all three strains suppressed the disease more effectively than the chemical fungicide. Indeed, for both year trials and cultivars combined, disease suppression potential, as compared to pathogen-inoculated and untreated control, ranged between 80.79 and 88.01% using the three-strain consortium relative to 70.00-82.07% achieved with single strains and 32.13-58.97% using fungicide. Plants grown in S. sclerotiorum-infected peat and challenged with the three-strain consortium were 38.36 to 80.95% taller than control ones whereas height increment noted using single strains and fungicide was of about 32.35- 79.01 and 29.62-51.85%, respectively. Aerial parts and root fresh weights of pathogen-inoculated and treated plants were enhanced by 51.59-74.69% and 54.00-78.12% using mixed strains and by 39.12-76.83% and 42.02-77.01%, respectively, using single strains compared to 24.04-53.05 and 12.74-67.05% noted on chemically treated plants. The effect of the three biocontrol agents was also examined on the composition of microbial communities inhabiting the rhizosphere of tomato plants. Results of the single strand conformational polymorphism (SSCP)-based profiling revealed that rhizosphere communities differed between cultivars only. However, the introduction of S. sclerotiorum or biocontrol agents did not cause detectable perturbations in the composition of fungal and bacterial communities inhabiting roots of treated tomato plants.