For many years, drug discovery studies in the field of epigenetics have focused mainly on specific enzymes such as histone deacetylases (HDACs). However, recently there has been increasing interest in small molecules targeting the multiprotein enzyme/transcription factor complexes that play key roles in the epigenetic control of gene expression. Aberrant function of these complexes often has pathological consequences. Here, we review small molecules that modulate the function of three well-known epigenetic complexes, namely, polycomb repressive complex 2 (PRC2), PRC1, and corepressor of RE1-silencing transcription factor (CoREST) complex, focusing on recent drug discovery studies targeting these epigenetic complexes.