The term non-coding RNA (ncRNA) refers to functional RNA molecules that, despite being transcribed from DNA, are not translated into proteins. These molecules can play an important role in the regulation of gene expression in the eukaryotic cell, and they can act either as long ncRNAs or being processed into small RNAs, being globally classified by their size, function, or genomic origin. In recent years, it has been found that diverse ncRNAs participate directly or indirectly in several epigenetic phenomena controlling different phenotypes within clonal cells, and in the specificity determination of various physiological processes. Although some of their mechanisms of action have been characterized, much remains to be known to understand the highly complex processes in which most of these molecules are involved. In this chapter, we discuss and illustrate examples of different ncRNAs that can interact with the plant epigenomic machinery or intervene in its function, leading to specific epigenetic, transcriptional, and physiological states. We explore the link between chromatin compaction, histone modifications, DNA methylation, gene silencing, and these molecules, which represent a high proportion of the cellular transcriptome.