Cytoplasmic male sterility plays an important role in utilization of crop heterosis. Screening of soybean for novel genes related to male sterility in soybean could provide a basis for studying the molecular mechanism of male sterility in plants. In this study, gene differential expressions between the cytoplasmic male-sterile line NJCMS1A and its maintainer line NJCMS1B in soybean were analyzed using cDNA-AFLP. A differentially expressed fragment, GmMF-T4A15, was isolated from large flower buds of NJCMS1B. By searching the soybean genomic library and PCR amplification, the cDNA fulllength sequence of 1 311 bp was obtained and named GmMF1. The expression characteristics of GmMF1 were studied by semiquantitative real-time PCR and real-time quantitative PCR. The results showed that GmMF1 was expressed highly in flower buds of NJCMS1B. The deduced protein contains 436 amino acids and shows high similarity to members of the DUF620 protein family with unknown functions in other plant species. It is predicted that the protein encoded by GmMF1 is localized in the nucleus.