Small RNA molecules have an important function in eukaryotic cells. Having a rather characteristic function and length, they are divided into several classes. The most abundant ones are miRNA, piRNA and siRNA. The model organism used for the study of biosynthesis and functions of these molecules is a plant A.thaliana. Heterochromatin interfering siRNA regulates transcriptional silencing of genes by inducing DNA methylation and dimethylation of H3K9. RNA directed DNA methylation (RdDM) is the main epigenetic pathway which is in plants directed by small RNA molecules. RdDM requires a specific transcription machinery which consists of two polymerases that are rather specific for plants - Pol IV and Pol V – and a large number of accompanying proteins whose function in RdDM is not entirely clear. The most important of these proteins are DCL3, RDR2 and AGO4. There are two possible ways of RNA silencing by using molecules. In the first instance, small RNA molecules cause transcriptional silencing of genes by forming heterochromatin and in the second, post-transcriptional silencing occurs because of mRNA degradation or inhibition of translation. Small RNA molecules are created by transcription from endogenous locus, as well as viral and transgenic nucleic acids. MiRNA and siRNA operate in somatic and generative cells in a broad spectrum of eukaryotic organisms where they participate in various functions - from regulation of transposons and biosynthesis of plant hormones to the development of the flower and leaves.