Recent advances in the technologies for developing genetically modified crops have highlighted the importance of epigenetic controls in plants. Several studies have suggested that double-stranded RNA (dsRNA) can induce sequence-specific DNA methylation and silence expression of target genes. Moreover, DNA methylation-mediated gene silencing can be stably transmitted to the next generation without dsRNA trigger constructs. By exploring and elucidating the molecular mechanisms behind these phenomena, we have achieved a greater understanding of epigenetic molecular mechanisms and this knowledge has provided the foundation for new techniques, the so-called New Plant Breeding Techniques (NBT). Further advances in our understanding of the molecular mechanisms of RNA-directed DNA methylation (RdDM) will enable improvements to these new techniques.