The structure of dye‐decolorizing peroxidase (DyP)‐type peroxidase differs from that of other peroxidase families, indicating that DyP‐type peroxidases have a different reaction mechanism. We have determined the crystal structures of DyP with ascorbic acid and 2,6‐dimethoxyphenol at 1.5 and 1.4 Å, respectively. The common binding site for both substrates was located at the entrance of the second cavity leading from the DyP molecular surface to heme. This resulted in a hydrogen bond network connection between each substrate and the heme distal side. This network consisted of water molecules occupying the second cavity, heme 6‐propionate, Arg329, and Asn313. This network is consistent with the proton transfer pathway from substrate to DyP.