This study was purposed to explore the application value of fluorescence in situ hybridization (FISH) detection in differential diagnosis of chronic myeloproliferative disorders (CMPD) and Ph(+) acute lymphoblastic leukemia (Ph(+) ALL), as well as in dynamic monitoring of minimal residual disease (MRD) after treatment. The BCR/ABL fusion gene of newly diagnosed and treated cases was detected by using BCR/ABL (ES) probe and BCR/ABL (DF) probe respectively. The results showed that among 49 newly diagnosed cases considered as CMPD, 28 cases met the criterion of CML morphologically, out of them 23 cases were eventually diagnosed to be CML and with morphological consistent rate 82.1% (23/28), the sensitivity and specificity all were 100% (23/23). The BCR/ABL positive rate of eventually diagnosed cases was 81.3% ± 17.7%. Among 13 cases received allogeneic haemopoietic stem cell transplantation (allo-HSCT), 9 cases achieved long-term disease-free survival and 4 cases relapsed, the several monitoring for whom after donor lymphocyte infusion (DLI) and imatinib treatment or allo-HSCT showed BCR/ABL negative. Among 16 cases treated with imatinib, 11 cases remained BCR/ABL negative after 1 year; 5 cases showed BCR/ABL positive during 6, 7 and 10 years after treatment, respectively, but out of them BCR/ABL positive in 1 case turned negative after allo-HSCT. It is concluded that the FISH is sensitive and specific diagnostic technique, the detection of BCR/ABL fusion gene in newly diagnosed and treated cases by using 2 different probes can help to fast and accurately determine the differential diagnosis for CML and Ph(+) ALL, and dynamically monitor the MRD after treatment with imatinib and allo-HSCT.