Bacteria endophytes are living microorganisms that live inside plant tissues without visible harmful symptoms, providing a mutualistic interaction. In this study, different bacterial endophytic strains were isolated from different plants primed to live in an arid area, namely, the Sahara Desert. Up to 27 of these strains were selected based on their ability to inhibit Botrytis cinerea growth in dual-culture assay and by bacterial volatiles. The results presented in this study show the capacity of most of the bacterial strains to protect Solanum lycopersicum against the pathogenic fungus B. cinerea, under different experimental conditions. Five of these strains induced susceptibility in tomato plants and no callose accumulation upon fungal infection, pointing to callose deposition as a protective mechanism mediated by endophytic bacteria. Moreover, there was a significant correlation between the bacterial strains inducing callose and the level of protection against B. cinerea. On the other hand, hormone production by bacteria does not explain the relationship between protection and the differences between the phenotypic results obtained in vitro and those obtained in plant experiments. Induced resistance is highly specific in the inducer-plant-stress interaction.