As a new class of biomaterials, most of the supramolecular hydrogels formed by small peptides require the attachment of a long alkyl chain, multiple aromatic groups, or strong electrostatic interactions. Based on the fact that the most abundant protein assemblies in nature are dimeric, we select short peptide sequences from the interface of a heterodimer of proteins with known crystal structure to conjugate with nucleobases to form nucleopeptides. Being driven mainly by hydrogen bonds, the nucleopeptides self-assemble to form nanofibers, which results in supramolecular hydrogels upon simple mixing of two distinct nucleopeptides in water. Moreover, besides being biocompatible to mammalian cells, the heterodimer of the nucleopeptides exhibit excellent proteolytic resistance against proteinase K. This work, as the first report that supramolecular hydrogelation triggered by mixing heterodimeric small nucleopeptides, illustrates a new and rational approach to create soft biomaterials.