We report a 76-year-old male patient with myelodysplastic syndrome (MDS) with a t(9;22) and deletion 20q only by FISH. Past medical history is significant for prostate cancer status post radiation therapy and a 28-pack-year smoking history. In 2016, the patient developed a DVT and incidentally was found to have a BCR::ABL1 (p210) by PCR analysis (level of 0.54% of the international scale). Subsequent bone marrow aspiration revealed a hypercellular bone marrow with a small monoclonal B-cell population morphologically consistent with chronic myelogenous leukemia (CML). FISH analysis demonstrated t(9;22) translocation and a loss of 20q12 in 5% of nuclei. The patient was started on nilotinib therapy. Follow-up BCR::ABL1 testing six months later did not detect BCR::ABL1; however, subsequent FISH analysis on bone marrow aspirates performed at one and seven years after initial diagnosis continued to show deletion 20q (1-3% of nuclei). Morphologic features of bone marrow aspirates have demonstrated a CML-type hypercellular bone marrow with myeloid/megakaryocytic hyperplasia and micromegakaryocytes. This case pinpoints the importance of comprehensive study when MDS is present with deletion 20q and a t(9;22), as it can be misdiagnosed as CML. While definitive therapeutic guidelines have yet to be established for this rare presentation of MDS, the use of tyrosine kinase inhibitors is under investigation.