A 62-year-old man was referred to our hospital due to pancytopenia and abnormal leukocyte fraction in December 2016. Bone marrow aspiration showed a massive proliferation of blast cells (96%) with rich myeloperoxidase-negative basophilic granules. He was diagnosed with acute basophilic leukemia, and an appropriate treatment for acute myelogenous leukemia was initiated. Blast cells were positive for minor BCR-ABL mutations, and chemotherapy using imatinib was initiated on day 7. The treatment was effective and complete remission was achieved on day 30. The ultrastructural features of blast cells showed typical basophilic granules with high electron density structure on electron microscopy. However, immunohistochemical analysis were positive for CD79a, PAX5, and TdT expression. Rearrangements of immunoglobulin heavy chain and T-cell receptor genes were detected, prompting the diagnosis of Philadelphia chromosome-positive acute lymphoblastic leukemia (Ph+ALL) with basophilic change. The patient continued to be treated with the imatinib combination regimen, as well as umbilical cord blood transplantation. The patient has currently achieved recurrence-free survival. This case represents a rare divergence between morphology and molecular condition.