An EST sequence containing MATH domain was selected from the SSH library constructed from the developing seeds. According to the sequence, a full cDNA was cloned using in silico cloning, named BnaMT1. BnaMT1 contained 1 209 bp and encoded a hydrophilic secretory protein of 402 amino acid residues containing a signal peptide, a transmembrane domain and two MATH domains. The estimated molecular weight and isoelectric point of the putative protein were 46 130.7 and 8.50, respectively. Phylogenetic analysis showed that BnaMT1 was closely related to Arabidopsis thaliana. The expression map was done in the whole plant and at different developmental stages of seeds by semiRTPCR. The results showed that BnaMT1 was expressed in leaf, flower and silique, but not in root and stem. BnaMT1 was expressed through the seed developmental stages with the expression first up-regulated, then kept at the highest level from 30 days to 35 days after flowering, and down-regulated afterwards. It was inferred that the function of BnaMT1 gene may be related to seed development.