MoCBP3 is a chitin-binding protein from M. oleifera seeds that inhibits the germination and mycelial growth of phytopathogenic fungi. This protein is highly thermostable and resistant to pH changes, and therefore may be useful in the development of new antifungal drugs. However, the relationship of MoCBP3 with the known families of carbohydrate-binding domains has not been established. In the present study, full-length cDNAs encoding 4 isoforms of MoCBP3 (MoCBP3-1, MoCBP3-2, MoCBP3-3 and MoCBP3-4) were cloned from developing seeds. The polypeptides encoded by the MoCBP3 cDNAs were predicted to contain 160 (MoCBP3-3) and 163 amino acid residues (MoCBP3-1, MoCBP3-2 and MoCBP3-4) with a signal peptide of 20-residues at the N-terminal region. A comparative analysis of the deduced amino acid sequences revealed that MoCBP3 is a typical member of the 2S albumin family, as shown by the presence of an eight-cysteine motif, which is a characteristic feature of the prolamin superfamily. Furthermore, mass spectrometry analysis demonstrated that MoCBP3 is a mixture of isoforms that correspond to different mRNA products. The identification of MoCBP3 as a genuine member of the 2S albumin family reinforces the hypothesis that these seed storage proteins are involved in plant defense. Moreover, the chitin-binding ability of MoCBP3 reveals a novel functionality for a typical 2S albumin.