Clonal hematopoiesis (CH) in aplastic anemia (AA) has been closely linked to the evolution of late clonal disorders, including paroxysmal nocturnal hemoglobinuria (PNH) and myelodysplastic syndromes (MDS)/acute myeloid leukemia (AML), even after successful immunosuppressive therapy (IST). With the advent of high-throughput sequencing of recent years, the molecular aspect of CH in AA has been clarified by comprehensive detection of somatic mutations that drive clonal evolution. Genetic abnormalities are found in ~50% of the patients with AA and, except for PIGA mutations and copy neutral loss-of-heterozygosity in 6p (6pUPD), most frequently represented by mutations involving genes commonly mutated in myeloid malignancies, including DNMT3A, ASXL1, and BCOR/BCORL1 Mutations exhibit distinct chronological profiles and clinical impacts. BCOR/BCORL1 and PIGA mutations tend to disappear or show stable clone size and predict significantly better response to IST and clinical outcome, compared to mutations in DNMT3A, ASXL1, and other genes, which are likely to increase their clone size and associated with a faster progression to MDS/AML and predict an unfavorable survival. High frequency of 6pUPD and overrepresentation of PIGA and BCOR/BCORL1 mutations are unique to AA, suggesting the role of autoimmunity in clonal selection. By contrast, DNMT3A and ASXL1 mutations, also commonly seen in CH in the general population, indicating a close link to CH in the aged bone marrow, in terms of the mechanism for selection. Detection and close monitoring of somatic mutations/evolution may help prediction and diagnosis of clonal evolution of MDS/AML and better management of patients with AA.