Reciprocal translocations involving the long arm of chromosome 7 are relatively rare cytogenetic aberrations in myelodysplastic syndrome (MDS) and acute myeloblastic leukemia (AML). A 44-year-old woman was initially given a diagnosis of de novo AML M6A with a normal karyotype. After achieving complete remission, she received allogeneic bone marrow transplantation from an unrelated male donor. Seven months later, pancytopenia appeared with 14.8% myeloblasts and dysplastic changes of neutrophils and megakaryocytes in the bone marrow. Chromosome analysis revealed complex karyotypes, with add(7)(q22) and add(9)(q34) detected in all abnormal metaphase spreads; spectral karyotyping revealed these chromosomal aberrations to be derived from a reciprocal translocation t(7;9)(q22;q34). Fluorescence in situ hybridization analyses showed that D7S486 at 7q31 was translocated to the der(9)t(7;9), and that the ABL gene at 9q34 remained on the der(9)t(7;9). Because the same translocation reappeared and sustained for more than 8 months after second stem cell transplantation, we revised the diagnosis as therapy-related MDS after allogeneic transplantation. The t(7;9)(q22;q34) was supposed to have a crucial role in the pathogenesis of MDS. Considering two other such reported cases of AML, the t(7;9)(q22;q34) may be a novel recurrent translocation in myeloid malignancies.