Epigenetic dysregulation plays a critical role in the pathogenesis of acute myeloid leukaemia (AML). The enzymes DNA methyl-transferase (DNMT3a) and Histone Lysine Demethylase (LSD1 or KDM1) are key molecules involved in transcription, DNA repair and differentiation of myeloid cells. In fact, DNMT3a is one of the most frequently mutated genes in acute myeloid leukaemia (AML) and LSD1 is essential in retinoic acid induced differentiation of myeloid cells. However, despite extensive investigation, it is not yet known their precise role in the evolution of AML clones. This information may be relevant for the successful management of the disease. In fact, it is unclear whether, mutated DNMT3a in AML clones has a dominant negative function and disrupts the formation of transcriptional complexes leading to aberrant methylation. Also, it is not known how LSD1 inhibition impacts on growth, differentiation and chemo-resistance of leukemic myeloid cells. In this review, we focus on the emerging evidences that correlate LSD1 and DNMT3a activity in acute myeloid leukaemia, their clinical relevance and how a deeper understanding of their biological function could lead to the discovery of new specific targets, some of which are currently tested in mechanism-based clinical trials.