In hybrids, genes inherited from both parents are typically expressed, producing intermediate phenotypes for many morphological phenotypes. However, some genes are expressed from the chromosomes inherited from only one parent. An example is nucleolar dominance, an epigenetic phenomenon in hybrids which describes the formation of a nucleolus (or nucleoli) at ribosomal RNA (rRNA) gene loci inherited from only one of the progenitors, regardless of whether that progenitor was the maternal or the paternal parent. Because rRNA genes are clustered by the hundreds, spanning millions of basepairs of chromosomal DNA, nucleolar dominance is one of the most extensive gene silencing phenomena known. We have shown that nucleolar dominance is due to uniparental rRNA gene silencing that involves concerted changes in DNA methylation and histone modification. Recently, we have begun to identify the chromatin modifying activities involved in rRNA gene silencing in Arabidopsis suecica, the allotetraploid hybrid of A. thaliana and A. arenosa in which the A. thaliana-derived rRNA genes are silenced. Histone deacetylases HDA6 and HDT1, one DNA methyltransferase and two methylcytosine binding proteins have been identified in the screens thus far. Other new evidence points to a role of small interfering RNAs, or siRNAs in controlling rRNA gene silencing in nucleolar dominance. Our current understanding of the mechanisms controlling nucleolar dominance will be presented.