Endophytic fungi can colonize several plant species and, in that way significantly alleviate the adverse effects of environmental stresses. Endophytic fungus of the order Sebacinales, Piriformospora indica, can be cultivated axenically and colonizes the root of a wide range of plants, not only promotes the growth, but also increases the plant tolerance to abiotic stress. The present study evaluated the effect of the inoculation of two tomato cultivars (Superluna and Caspian) with P. indica to ameliorate the effect of drought stress by analyzing plant growth, and some morpho-physiological parameters. Also, the expression and promotor analysis of LEA14, TAS14, GAI, and P5CS genes was investigated. Results showed that drought stress decreases shoot fresh and dry weight, relative water content and proline level. The tolerant cultivar (Caspian) had a higher level of Shoot weight, RWC and proline compared to the sensitive cultivar (Superluna). Likewise, P. indica colonization increased the measured factors in both tomato cultivars under normal and drought stress conditions. Also, gene expression analysis showed that except for the GAI gene, the expression of other genes was increased in drought and fungus treatments, and the interaction effect of the two treatments increased the expression of these genes. The results suggested that the symbiotic association between plant and fungus could help the tomato plants to tolerate the drought stress through physiological and molecular pathways, opening up a window of opportunity for its application in sustainable agriculture.