Drought stress is currently the most serious challenge to global food security and agricultural productivity. Desert actinobacteria have gained attention as potential candidates for enhancing plant growth in water stress environments. In this regard, a desert actinomycete, namely Modestobacter caceresii strain KNN 45-2bT, was selected to investigate its plant growth promoting abilities and drought tolerance. Next, this desert strain was inoculated to tomato (Lycopersicum esculentum Mill.) under drought, and the results included increases in root length, shoot and root fresh weight, shoot and root dry weight, total fresh weight and dry weight, fruit weight, proline accumulation, total soluble sugar content and trolox content. Stress treatments on the bacterized tomato plants also resulted in the reduction of hydrogen peroxide accumulation. Putative proteins coding sequences conferring plant growth promoting (PGP) traits (IAA production, phosphate solubilization, siderophore production, nitrogen fixation) and drought response (biosynthesis of proline metabolism, oxidative and osmotic stress response) were also detected from their genomic analyses. In conclusion, these results provide credence to the idea that the inoculation of tomato plants with plant beneficial desert actinomycete is an effective method of combating the negative effects of drought stress.