In the present study, we report a case of a 58-year-old female patient presenting with Philadelphiachromosome (Ph)-negative blast cells and Ph -positive mature cells at diagnosis. The complete blood cell count showed the patient had a white blood cell count of 35.5 × 109/L and a differential blast count of 62%. A bone marrow biopsy showed closely packed marrow with blast cell infiltration. Blasts were weakly positive for MPO stain, but negative for PAS and ANAE stains. Moreover, blasts tested positive for CD34, CD13, CD117, CD15, CD33, and CD7 and negative for TdT, CD3, CD22, and CD19 in cytometric immunophenotyping experiments. The patient, who had the karyotype 46,XX,t(9;22) (q34;q11.2) /45,XX,inv(3)(q21q26.2),-7, was therefore diagnosed as having AML. Fluorescence in situ hybridization (FISH) showed a decrease in Ph-positive clones and an increase in monosomy 7- positive clones after CD34-positive cell enrichment, suggesting that the blasts were primarily Phnegative. This case highlights the necessity of analyzing the cytogenetic characteristics of blasts to better understand the nature of the disease when only a fraction of the cells are Ph-positive.