Epigenetic deregulation has been recognized as an important contributor to cancer initiation and progression as most tumors harbor both genetic and epigenetic abnormalities. Inhibiting epigenetic proteins represents a novel approach in cancer drug discovery and more profound efficacy and less resistance are expected since multiple signaling pathways can be modulated as a result of inhibiting a single epigenetic target. Histone methyltransferases (HMTs) are an important component in epigenome and HMT inhibitors are being pursued intensely by both pharmaceutical industry and academic institutions. In this article we will provide an update on the drug discovery effort on several key HMTs.