Chimeric transcription factors are a hallmark of human leukemia, but the molecular mechanisms by which they block differentiation and promote aberrant self-renewal remain unclear. Here, we demonstrate that the ETO2-GLIS2 fusion oncoprotein, which is found in aggressive acute megakaryoblastic leukemia, confers megakaryocytic identity via the GLIS2 moiety while both ETO2 and GLIS2 domains are required to drive increased self-renewal properties. ETO2-GLIS2 directly binds DNA to control transcription of associated genes by upregulation of expression and interaction with the ETS-related ERG protein at enhancer elements. Importantly, specific interference with ETO2-GLIS2 oligomerization reverses the transcriptional activation at enhancers and promotes megakaryocytic differentiation, providing a relevant interface to target in this poor-prognosis pediatric leukemia. Display omitted •The GLIS2 moiety of ETO2-GLIS2 oncoprotein controls the megakaryocytic identity•Human AMKL oncogenes often cause GATA/ETS functional imbalance•ETO2-GLIS2 binds enhancer regions together with the ERG transcription factor•The NHR2 interface is essential for maintenance of ETO2-GLIS2-driven leukemia Thirant et al. show that the ETO2-GLIS2 fusion protein found in acute megakaryoblastic leukemia confers megakaryocytic identity via the GLIS2 moiety, but requires both ETO2 and GLIS2 domains to drive self-renewal. Disruption of ETO2-GLIS2 oligomerization inhibits the maintenance of ETO2-GLIS2+ human AMKL blasts.