Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) catalyzes the interconversion of glyceraldehyde 3-phosphate and 1,3-diphosphoglycerate during glycolysis and gluconeogenesis. In most organisms, a single GAPDH is responsible for the reaction. However, Bacillus subtilis has two isoforms of this enzyme, namely, GapA and GapB, each of which catalyzes the reaction in the opposite direction. GapA uses NAD⁺ as a cofactor, whereas GapB prefers NADP⁺. In this study, we report the crystal structure of GapB at 2.3 Å resolution. X-ray diffraction of GapB crystal was observed up to 2.0 Å resolution, and its structure was determined using molecular replacement. Its overall fold and quaternary structure (a homo-tetramer) were similar to that of the reported GAPDHs. The S-loop was missing because of the absence of the NADP⁺.