DNA information and sequences of plant genomes always need to be stable. Hence, the improvement of a resistant system in plant genomes is necessary to avoid a restriction of conserved DNA sequences. The protection system in stressed plant cells is activated rapidly and dynamically through the RNA directed DNA methylation (RdDM) pathway to control the stress effects before any damage occurs in plant genomes. The RdDM pathway is a key process including short interfering RNA (siRNA), causes epigenetic modification in plant genomes. The modification system of plant cells such as cytosine methylation is associated with histone modification through the different roles in regulating of the gene expression and genome structure. The environmental stresses such as plant pathogenic infections can change the level of DNA methylation in plant genomes. This phenomenon could influence plant ability in more adaptation to different environmental conditions. The DNA methylation in plant cells is facilitated by Domain rearrange DNA methyltransferase (DRM2) which plays a key role in control and manage of the enzymatic process of RdDM pathway. In this study, we provide an overview of function and variation of DNA methylation under different environmental stresses and the key roles of DRM2 in RdDM pathway which complete the pathway reactions through DNA methylation process in plant cells.