Peptide self-assembly provides a useful approach to control the organization of functional molecular components, as relevant to future opto-electronic or photonic nanostructures. In this article, we report on the discovery of efficient energy transfer nanostructures using a dynamic combinatorial library (DCL) approach driven by molecular self-assembly, demonstrating selection and amplification of effective energy transfer nanostructures from complex mixtures of dipeptide derivatives. By taking advantage of an enzyme-catalysed fully reversible amide formation reaction, we show that how gelation shifts the equilibrium in favour of the formation of short aromatic dipeptide derivatives in DCL system, as confirmed by reversed-phase high pressure liquid chromatography (HPLC), fluorescence emission spectroscopy, atomic force microscopy (AFM), transmission force microscopy (TEM) and circular dichroism (CD) spectroscopy. This approach enabled us to identify a bi-component donor/acceptor hydrogel, which forms within minutes and exhibits highly efficient energy transfer.