Abstract d-Arabinofuranosidases (Arafases) degrade the arabinan in the cell wall of acid-fast bacteria like Mycobacterium. Synthetic arabinan fragment probes could be used to investigate the function of d-Arafases, whose synthetic studies had been reported previously. The homologue of one of the arabinan-degrading enzymes, exo-α-d-Arafase, was identified as BBDE_2040 from Bifidobacterium dentium. BBDE_2040, which is a homologue of α-d-Arafase, was also observed to hydrolyze α-d-fructofuranosides (Fruf), whose linkage is found in food. In this paper, we present synthetic studies and structural analysis of the α-d-Araf and α-d-Fruf derivatives as substrates and products of the enzymatic reaction for a thorough examination of BBDE_2040. The results indicated that BBDE_2040 is a glycoside hydrolase (GH) family 172 difructose dianhydride I synthase/hydrolase and an anomer-retaining GH.