It is hard to discriminate myelodysplastic syndrome(MDS) from many benign hematological diseases. To identify the methylation status of zo-1 gene in MDS, the methylation specific PCR (MS-PCR) and reverse transcription-PCR (RT-PCR) were applied to detect the MDS cell line MUTZ-1, bone marrow of a healthy donor and an aplastic anemia patient. MS-PCR was also employed to detect the bone marrow of 72 patients with benign hematological diseases, 35 MDS-RA patients, and 20 MDS-like patients. The results showed that MDS cell line MUTZ-1 displayed complete methylation of zo-1 promoter without mRNA expression. Inversely, a patient with benign hematological disease and a donor with normal bone marrow showed complete unmethylation of this gene with unaffected mRNA expression. No zo-1 promoter methylation was detected in patients with benign hematological diseases, while aberrant hypermethylation of zo-1 gene promoter were found in 48.6% (18/37) of MDS-RA patients. The positive rate of zo-1 methylation in MDS-RA patients was higher than that in patients with benign hematological diseases (p < 0.05). Seven suspected MDS patients manifested hypermethylation status of zo-1 gene (7/20), 2 were followed up for 1 year and transformed into MDS. It is concluded that relatively high hypermethylation rate of zo-1 promoter is observed in MDS-RA, and no methylation in patients with benign hematological diseases. Therefore, zo-1 gene hypermethylation may be served as a useful epigenetic marker in the differential diagnosis for MDS.