Peptides are an important source of nutrients for bacteria. In some bacteria, deletion or inhibition of peptide transporters results in reduced pathogenicity, virulence or adherence to host, which is why peptide transporters can be considered targets for the development of novel antimicrobial agents. Two peptide ATP Binding Cassette (ABC) transporters systems, annotated dpp (for dipeptides) and opp (oligopeptides), have been reported in H. pylori. Here we present the X-ray crystal structure DppA from H. pylori SS1 - the periplasmic substrate-binding protein (PBP) of one of the two systems. The structure of the protein co-purified with a tetrapeptide has been solved using a molecular replacement method to a resolution of 1.8 Å. It comprises two globular lobes connected by two linkers at the hinge identifying it as type II/ cluster C PBP fold. The peptide ligand is trapped in a deep cavity between the lobes and binds to protein through interactions mainly mediated by the peptide main chain. Comparison of the DppA-tetrapeptide structure with that of the unliganded structure of DppA from Pseudoalteromonas sp. reveals a ~30° hinge-bending motion. Mass spectrometry analysis revealed that H. pylori DppA binds peptides of up to eight amino acids in length. Detailed analysis identified the structural features that allow DppA to accommodate longer peptides, in contrast to Dpps from other bacteria. Furthermore, this analysis allowed us to identify residues important for ligand recognition and binding. Biophysical assays demonstrated that the protein binds di-, tetra- and hexapeptides with Kd in a low-micromolar range. Altogether, our work sheds light on the structural basis of ligand recognition in DppA, which provides a better understanding of the mechanisms of peptide import in H. pylori.