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Stress can exert its effect on the organism not only via physiological response pathways but also via genomic and indeedepigenetic responses. Environmental signals affect the extent of DNA methylation by their interaction with the plant. Ingeneral, imposing different biotic and abiotic stresses to the plants leads to increased gene methylation and thus leading todegeneration of genome activity. Keeping this in view, the two high yielding lowland rice cultivars IR 20 and CO 43 and thetwo rice cultivars with drought tolerant traits PMK 3 and Paiyur local were raised in pots under water stress and irrigatedconditions. Genomic DNA from the four cultivars was subjected to restriction digestion with methylation sensitiveisoschizomers MspI and HpaII. In all the cultivars, internal methylation (5’-CmCGG-3’) was found to be dominant in riceleaves suggesting a high frequency of mCpG dinucleotide as compared to mCpC dinucleotide in the 5’-CCGG-3’ sequence inrice DNA. Drought susceptible cultivar (IR 20) under stress shows higher MspI and HpaII digestion than irrigated control,suggesting that demethylation have occurred under stress thereby altering the genome activity. But in case of drought tolerantcultivars PMK3 and Paiyur local, HpaII digestion was found to be lesser under stress conditions than irrigated control,suggesting that methylation have occurred under stress thereby gene expression gets altered. Thus, a change in methylationlevel was noticed among the rice cultivars under water stress and control conditions.