DNA methylation at cytosine residues governs the regulation of stress responsive genes in plant for self-protection against various environmental abiotic stresses. Here, we analyzed the epigenetic consequences of drought and salinity on cytosine methylation dynamics of promoter regions of stress responsive Germin-like protein genes in rice (Oryza sativa). The bisulfite sequencing technique was employed to identify differential methylation status at cytosine residues in selected promoter regions of three OsGLP genes (OsGLP4-1, OsGLP8-10 and OsGLP8-12) in leaves and roots of two elite Indica rice cultivars (tolerant KS282 and sensitive Super Basmati) under drought and salt stress. Our results identified cultivar, tissue and stress-dependent differentially methylated cytosine residues, however, the extent of methylation was found to be different depending upon CGN, CHG and CHH sequence contexts. Among all three OsGLP genes, the promoter region of OsGLP8-12 was detected with the most heavily methylated and significantly differential methylated sites depending upon types of variety, tissue or stress conditions. However, no methylated site was detected in the promoter region of OsGLP4-1. Moreover, in the promoter regions of OsGLP8-10 and OsGLP8-12, several differentially methylated sites in response to stress treatments were identified either near or within cis-regulatory elements (CREs) related to abiotic stress. This indicated the association between methylation in the promoter regions and regulation of OsGLP genes which might be a key mechanism associated with their regulation under abiotic stresses in contrasting rice cultivars.