Although acute transformation to acute myeloid leukemia represents a well-established form of disease progression in myelodysplastic syndromes (MDS), the progressive development of proliferative features with a phenotypic shift to a myelodysplastic/myeloproliferative neoplasm such as chronic myelomonocytic leukemia developing from a prior MDS has also been observed. However, transition from a MDS to an atypical chronic myeloid leukemia BCR-ABL1 negative (aCML) is exceptionally rare. Herewith we report one such case, describing its clinical, morphologic and molecular correlates. The observed molecular progression which paralleled the phenotypic shift, partially elucidates the pathogenetic mechanisms involved in this rare type of disease progression.