Chemists and material scientists are interested in complex biological systems and morphologies for fabrication of new materials. Bioinspired design of short peptide conjugates produces various self-assembled structures, depending on their structural diversity. Phe-Phe aromatic dipeptide is an interesting candidate for designing variety of molecular scaffolds. This report describes the synthesis of two symmetrical peptide conjugates by a coupling with C2 and C3 symmetric functional linker's, which spontaneously generate different self-assembled ultra-structures. C2 Symmetric, ethylene diamine linker, conjugated two Phe-Phe dipeptides and produced Phe-Phe-EDA-Phe-Phe (5), which undergoes spontaneous self-assembly to form fibrillar morphology, while C3 symmetric tris(2-aminoethylamine) conjugated three Phe-Phe dipeptides, produced (Phe-Phe)3TREN (7) resulted in spherical morphology structures interconnected by fibers. A rational design of two peptide conjugates, by introducing two different linker's, direct different self-assemble pathway, which result in distinct morphologies. © 2013 Elsevier Ltd. All rights reserved.