We report a case of a 72 year old female who was referred to our institution in August 2010 for Myelodysplastic syndrome (MDS) with a deletion of part of the long arm of chromosome 5 [i.e., del(5) (q12q33)]. In June 2014, she transformed to Chronic Myelogenous Leukemia (CML), where cytogenetic and FISH analysis of the bone marrow (BM) revealed the del(5q) in 1.5% of nuclei and a complex BCR/ABL1 translocation [i.e., 45,XX,t(9;15;22)(q34;p10;q11.2),-22]. Six weeks later, in July 2014, she transformed to an Acute Myelogenous Leukemia (AML) blast crisis. RT-PCR was positive for BCR/ABL1 transcript. The patient was treated with a tyrosine kinase inhibitor, Nilotinib, then had a haploidentical allogeneic bone marrow transplant from her son, and was in remission after treatment. However, throughout the course of nine subsequent cytogenetic analyses, the patient continued to undergo clonal chromosome evolution, even during remission. Transformation from MDS del(5q) to CML with rapid progression to blast crisis has rarely been reported. To our knowledge, transformation with this complex translocation has never been described. Here we describe these rare cytogenetic findings and discuss possible mechanisms involved in the persistent and evolving clonal cytogenetic abnormalities seen during the clinical course of the disease.