Although many nanomaterials have been prepared in vitro by mimicking biomineralization, the biomimetic synthesis of hybrids with both well-ordered nanostructures and specific functions is still in its infancy. A short designed peptide amphiphile I₃K can form uniform and stable nanofibers in aqueous solution, with a surface enriched in cationic lysine residue. In the present study, we have demonstrated that the peptide nanofibers could direct the synthesis of MnO₂ nanowires under mild conditions. By varying the concentration of manganese precursors (KMnO₄ and Mn(NO₃)₂), uniform branched MnO₂/peptide hybrid nanowires with high porosity and a large specific surface area were obtained. The well-defined MnO₂ hybrid nanowires showed significantly improved electrochemical supercapacitive properties relative to compact MnO₂ nanowires and urchin-like MnO₂ spheres. Their specific capacitance could attain a higher value of 421 F g⁻¹ and retained about 93% of the initial capacitance after 2500 cycles at a scan rate of 5 mV s⁻¹, and remained little changed during the process of progressively varying the current density. Furthermore, the electrode prepared from the uniform MnO₂ hybrid nanowires showed an excellent reversibility and a reasonably high-rate capability during the charge/discharge process. Such a study provides a new methodology to prepare functional MnO₂ nanostructures under mild conditions that can be used in electrochemical energy storage.