Acute myeloid leukemia (AML) is a heterogeneous disease, the onset of which involves a variety of chromosomal abnormalities and gene mutations. In recent years, the use of next-generation sequencers has facilitated intensive exploration of gene mutations resulting in the discovery of many AML-related gene mutations, and in clarifying the clonal evolution process of relapse. Epigenetic regulatory gene mutations have occurred in pre-leukemic cells with normal differentiation potential, and the acquisition of numerous genetic mutations was found to be strongly associated with AML onset, with further co-mutations contributing to clonal diversity and leading to the generation of treatment-resistant clones. As a result of these fruitful findings, the gene mutations of AML are becoming useful as not only prognostic factors but also the targets of molecular medicines such as FLT3 and IDH inhibitors. Most notably, several guidelines have proposed a prognostic classification that groups FLT3ITD, NPM1 mutation, and CEBPA mutation together under conventional chromosomal aberrations. This review outlines recent findings pertaining to the gene mutations in AML.