Deciphering the mutational patterns and/or the biomarkers that might predict clinical response in patients with myelofibrosis is primordial to make treatment decisions. In this report, we discuss the clinical history, pathological evaluation, and genomics findings in a patient with JAK2-positive myelofibrosis who developed a secondary myelodysplasia after hematopoietic stem cell transplantation and JAK1/2 inhibitor treatment. Using next-generation sequencing, a paired comparison of relapse-specific versus primary tumour mutations highlighted the dynamic clonal evolution at relapse, showing concurrently the complete eradication of the JAK2-positive clone and the expansion of a second JAK2-negative clone with additional mutations. Importantly, another unexpected finding was that myelodysplasia was not secondary to allogeneic transplantation as relapse was driven by the overgrowth of a preexisting mutated clone, probably fostered by initial treatment options. This case underlines the fact that determining the genetic changes associated with the primary disease and its evolution is crucial to accurately correlate variants frequency to treatment decision and/or treatment response.