Epigenetics is the study of heritable changes in gene function that occur without a change in the DNA sequence. In recent years, this field has attracted much attention as more epigenetic controls of gene activities are being discovered. Such controls involve a complex interplay of DNA methylation, histone modifications, and RNA-mediated pathways from non-coding RNAs, notably silencing RNA (siRNA) and microRNA (miRNA). Epigenetic regulation is not only important for generating diversity of cell types during plant development, but also in maintaining the stability and integrity of their respective gene expression profiles. Although epigenetic processes are essential for development and differentiation, they can become misdirected leading to diseases, especially cancer. DNA methylation, histone modifications, and RNA-associated pathways are generally associated with the initiation and maintenance of silencing of gene expression and interact to each other to effect heritable silencing Sensing environmental changes and initiating a gene expression response is of paramount importance for plants as sessile autotrophs. Although epigenetic mechanisms help to protect plant cells from parasitic elements such as transposons, this defense can complicate the genetic engineering process through transcriptional gene silencing. Epigenetic phenomena have economic relevance in the case of somaclonal variation: a genetic and phenotypic variation among clonally propagated plants from a single donor genotype. The success of sequencing projects on model plants has created widespread interest in exploring the epigenome in order to elucidate how plant cell execute the information kept in the genome. New techniques are making it easier to map DNA methylation patterns on a large scale and the results have already provided surprises.