rDNA is an array of tandemly repeated genes controlling cellular ribosomes’ biosynthesis, therefore determining translational level of overall proteins and being closely linked with cellular growth and metabolism. Because of the multi-copy feature, the transcription activity of rDNA repeats is not only adjusted by general transcription mechanism, but also finely regulated by multiple epigenetic mechanisms. Generally, rDNA is divided into two epigenetic states, active and silent state, relating to active chromatin marks and heterochromatin marks respectively. In recent years, a poise state has been found, which enriches the research of epigenetic mechanism in rDNA regulation. H3.3, a hot topic in recent years, is a variant of histone H3, which has been reported that might incorporate into active rDNA by its chaperone HIRA. However, more devotion is required to explore whether silent rDNA is maintained by H3.3 as well. Another regulator is CTCF, an insulator component that occupying between repeated rDNA units. Whether CTCF is involved in regulating the transcription of rDNA is still unknown. In this review, we present our current knowledge of the mechanisms in rDNA epigenetic regulation, and propose new hypotheses of regulatory mechanism that might exist in this process.