In nature, plants are frequently exposed to various stress. Since plants are sessile organisms, their ability to cope with stress is crucial. It is known that epigenetic mechanisms such as cytosine methylation play significant role in plant stress response. In this study, we evaluated the morphological, physiological and molecular responses of Arabidopsis thaliana plant and call after NaCl and abscisic acid (ABA) treatment in vitro. While plants were morphologically affected, on the contrary there was no morphological change in calli. It is known that phenotypic changes under stress conditions are also dependent on epigenetic modifications such as DNA methylation, chromatin modifications and siRNA mediated mechanisms in addition to DNA sequence variants. In this context, we analysed global DNA methylation patterns and their influence on transcription in four methylation related genes. We found that while NaCl application caused hypomethylation in plants, ABA application did not make a change in genomic methylation. According to the qPCR results, the most obvious difference was the increase in expression of Pol IV after NaCl application in both samples and for the DRM2 gene is the increase in plant samples after ABA application. In conclusion, although we found evidence for epigenetic regulation after NaCl treatment, but not related to ABA treatment. These results demonstrate the mutual interaction between morphophysiology, DNA methylation and the associated gene expression, and provide insight into the abiotic stress response of Arabidopsis.