This study was conducted to analyze the osmotic stress-induced polymorphism in the two stress-responsive genes [TSW12 (non-specific lipid transfer protein1) and TAS14 (abscisic acid and environmental stress-inducible protein)] of somaclonal variant cells of tomato (Lycopersicon esculentum L.). The cells were subjected to the sublethal concentration of mannitol (250 mM) and the mutations of TSW12 and TAS14 genes were investigated by PCR using specific (upstream and downstream) primers for each gene. The amplification products were sequenced to uncover the mutations. Mutation effect on protein structure and function was predicted using SIFT PolyPhen-2, PANTHER, and PredictSNP tools. The results showed nine mutations in TSW12 and TAS 14 genes (6 and 3, respectively), and 7/9 were SNPs while the other two are frameshift mutations. Among them, a couple of SNPs mutations was novel; 104C>T on TSW12 and 146G>C on TAS14. Prediction analysis of the 3D structure of the amino acids showed that most SNPs were benign. The subjection of somaclonal variant cells to drought stress resulted in slight genetic modifications of the two investigated responsive genes, and therefore, neglected changes of corresponding proteins. This result demonstrated that mutations reported in the examined genes may have a minimal effect on the role of these genes in controlling drought injury in tomato.