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Abstract Background The plant pathogenic fungi, Alternaria solani and Fusarium oxysporum, are considered among the fungal pathogens which cause severe damages to tomato plants. The application of chemicals fungicides reduced fungal infection and entails great risks to human health and to the environment. Using biological control agents is considered one of the most effective techniques which suppress fungal pathogens and preserve the environment. The beneficial bacterium, Lysobacter enzymogenes, is applied as a biocontrol agent against different plant pathogens. Results The present work was carried out, under laboratory conditions, to investigate the efficacy of L. enzymogenes different concentrations of the strain ch3B10 on controlling the linear growth of A. solani and F. oxysporum compared to using the fungicide Benlate®. Treatment with Benlate® and the highest concentration (2 × 108 CFU/ml) of L. enzymogenes strain ch3B10 showed the highest inhibition of 70.6–94.0% on linear growth of all the tested fungi. Also, treatments with two concentrations (2 × 106 and 2 × 107 CFU/ml) of L. enzymogenes strain ch3B10 inhibited linear growth of all tested fungi by means of 47.1–69.7%. The low concentration of 2 × 103 CFU/ml of the strain ch3B10 resulted in the lowest linear growth inhibition 19.8–28.1% in all tested than the check treatment. Conclusion Further experiments under both greenhouse and field conditions are needed to approve the efficacy of the strain ch3B10 as an effective bioagent and ecologically safer approach than chemical treatments.