As the first known structures of a glycoside hydrolase family 54 enzyme, we determined the crystal structures of free and arabinose-complex forms of α-L-arabinofuranosidase from Aspergillus kawachii IFO4308 (AkAbf54). AkAbf54 comprises two domains: a catalytic domain and an arabinose-binding domain. The catalytic domain has a β-sandwich fold slightly similar to those of clan-B glycoside hydrolases. The arabinose-binding domain has a β-trefoil fold similar to that of carbohydrate-binding module (CBM) family 13. However, the arabinose-binding domain shows a number of distinctive characteristics from those of CBM family 13. Therefore, it was classified into a new CBM family, CBM42, and was referred to as AkCBM42. In the arabinose-complex structure, one of three arabinofuranose molecules bound to the catalytic domain through many interactions. Interestingly, a disulfide bond formed between two adjacent cysteine residues recognized the arabinofuranose molecule. From the location of this arabinofuranose and the results of a mutation study, the nucleophile and acid/base residues were determined to be Glu221 and Asp297, respectively. The other two arabinofuranose molecules bound to AkCBM42. The O1 atoms of both these arabinofuranose molecules are exposed to the solvent, indicating that AkCBM42 binds arabinofuranose residues linked to the xylan backbones of arabinoxylans. Binding assay and affinity gel electrophoresis analysis with insoluble polysaccharides, and ITC analysis with mono- or oligosaccharides revealed a unique function of AkCBM42. This is the first example of a CBM that can specifically recognize the side-chain moieties of branched polysaccharides.