•Autologous transplantation allows clonal hematopoiesis to escape mutagenic chemotherapy and be reinfused to expand to neoplasm.•Distinct chemotherapies can promote the selection and acquisition of genomic drivers in therapy-related myeloid neoplasms. Display omitted Patients treated with cytotoxic therapies, including autologous stem cell transplantation, are at risk for developing therapy-related myeloid neoplasms (tMN). Preleukemic clones (ie, clonal hematopoiesis CH) are detectable years before the development of these aggressive malignancies, although the genomic events leading to transformation and expansion are not well defined. Here, by leveraging distinctive chemotherapy-associated mutational signatures from whole-genome sequencing data and targeted sequencing of prechemotherapy samples, we reconstructed the evolutionary life-history of 39 therapy-related myeloid malignancies. A dichotomy was revealed, in which neoplasms with evidence of chemotherapy-induced mutagenesis from platinum and melphalan were hypermutated and enriched for complex structural variants (ie, chromothripsis), whereas neoplasms with nonmutagenic chemotherapy exposures were genomically similar to de novo acute myeloid leukemia. Using chemotherapy-associated mutational signatures as temporal barcodes linked to discrete clinical exposure in each patient’s life, we estimated that several complex events and genomic drivers were acquired after chemotherapy was administered. For patients with prior multiple myeloma who were treated with high-dose melphalan and autologous stem cell transplantation, we demonstrate that tMN can develop from either a reinfused CH clone that escapes melphalan exposure and is selected after reinfusion, or from TP53-mutant CH that survives direct myeloablative conditioning and acquires melphalan-induced DNA damage. Overall, we revealed a novel mode of tMN progression that is not reliant on direct mutagenesis or even exposure to chemotherapy. Conversely, for tMN that evolve under the influence of chemotherapy-induced mutagenesis, distinct chemotherapies not only select preexisting CH but also promote the acquisition of recurrent genomic drivers. Patients receiving cytotoxic chemotherapy and autologous transplantation may develop therapy-related myeloid neoplasms (tMN). Diamond and colleagues analyzed the genomic evolution of tMN to distinguish between chemotherapy-induced mutations and evolution from previous clonal hematopoiesis. tMN arising after mutagenic chemotherapy shows a complexity of new mutations, while tMN arising after nonmutagenic chemotherapy resembles de novo acute leukemia. The trajectory of tMN may arise from the acquisition of new mutations, selection of previously mutated clones, or the expansion of mutant clones transferred from the apheresis product.