Maize, a moderately salt sensitive crop, first experiences osmotic stress that cause reduction in plant growth under salt stress. Fluctuation in cell wall elongation is one of the reasons of this reduction. Along with others, two important proteins expansins and xyloglucan endotransglucosylase are involved in regulation of cell wall elasticity, but the role of epigenetic mechanisms in regulating the cell wall related genes is still elusive. The present study was conducted with the aim of understanding the role of DNA methylation in regulating ZmEXPB2 and ZmXET1 genes. One salt sensitive and one salt tolerant maize cultivar was grown under hydroponic conditions at different levels of salt stress: T1 = 1 mM (control), T2 = 100 mM and T3 = 200 mM in three replicates. DNA and RNA were extracted from roots. After bisulfite treatment, Methyl Sensitive PCR was used for the DNA methylation analysis. It was revealed that fragment in promoter of ZmEXPB2 gene showed high level of DNA methylation under T1 in both varieties. Comparison of different stress treatments revealed decrease in DNA methylation with the increase in salt stress, significantly lower methylation appearing in T3. Similarly, the fragment in promoter of ZmXET1 gene also showed high levels of DNA methylation in T1. When different treatments were analysed, this gene significantly hypomethylated at T2 which continued to decrease in T3 in sensitive variety but remain stable in tolerant variety. Although, further in-depth analysis is required, our results demonstrate region-specific and genotype-specific methylation shift in the promoter of the ZmEXPB2 and ZmXET1 genes when subjected to the salt stress confirming the epigenetic regulation of these genes under stress conditions.