Salinity affects the growth and development of plants by disturbing their normal metabolism. Rice plants have unique stress adaptation mechanisms with wide range of variation in salt tolerance level among genotypes. DNA methylation is one of the epigenetic mechanisms for regulation of gene expression in response to various environmental stimuli. We studied the effect of salinity on DNA methylation pattern in root and shoot of six rice genotypes differing in salinity response (salinity susceptible: Bengal, IR29, Nipponbare and salinity tolerant: Pokkali, Nonabokra, Geumgangbyeo), using methylation sensitive amplification polymorphism technique. Salt stress affected the overall methylation/demethylation of DNA in root, shoot of all genotypes. However, under salinity stress, full methylation was more than hemi-methylation both in root and shoot of all the six rice genotypes irrespective of their level of salt tolerance. Except Nipponbare, a general trend of more demethylation was observed in shoot than root in all the genotypes under salinity. Nucleotide sequences of 13 polymorphic methylated/demethylated DNA fragments showed gene-body specific DNA methylation changes. Out of three DNA fragments homologous to retrotransposon genes, two got demethylated in the shoot of salinity susceptible genotypes, Nipponbare, and IR29 whereas one fragment was methylated in shoot of salinity tolerant, Nonabokra, indicating genotype and shoot specific methylation alteration. Transcript abundance study of six selected fragments belonging to stress responsive genes category showed genotype and organ specific differential expression under salinity. Thus, differential epigenetic response under salinity may be responsible for differences in stress adaptation behavior in tolerant and susceptible rice genotypes.