The combination of a naphthalene diimide (NDI) group and a single amino-acid of serine (Ser) or lysine (Lys) can be used to promote the formation of a supramolecular hydrogel, which indicates the aromatic amino acid is not necessary to be used in the structural design of NDI-capped small molecule hydrogelators. An equimolar ratio of NDI-Ser and NDI-Lys can form a stable hydrogel under neutral conditions and its gel-to-sol transition temperature is higher than 37 °C. This work, as the first example of NDI-containing hydrogelators without aromatic rings in the side chains of amino acids, illustrates a new approach to design NDI-capped supramolecular hydrogels.