Polyaniline/Polypyrrole (PANi/PPy) composite nanofibers with core–shell structures were prepared by covering PPy thin layers on the surface of PANi nanofibers as high–performance electrode materials for supercapacitors in neutral aqueous electrolyte. Core part of PANi was firstly synthesized through chemical oxidative polymerization of aniline monomers in the presence of phenylenediamine (PDA) isomers including o–phenylenediamine (o–PDA), m–phenylenediamine (m–PDA) and p–phenylenediamine (p–PDA) without the assistance of any templates or usage of organic solvents, and then the shell part of PPy was fabricated by in–site chemical oxidative polymerization of pyrrole with the above–mentioned PANi as a seed. PANis and corresponding composite were investigated by field–emission scanning electron microscopy, ultraviolet–visible spectroscopy, Fourier transform infrared and Raman spectrometry, and wide angle X–ray diffractometer. Furthermore, electrochemical behaviors of PANis in H2SO4 and Na2SO4 electrolyte as well as corresponding composites in Na2SO4 electrolyte were tested by cyclic voltammetry, galvanostatic charge–discharge techniques and electrochemical impedance spectroscopy. It is found that compared with pure PANi prepared without PDA isomers, the incorporation of o–PDA and p–PDA is helpful to improve the electrochemical property of PANi nanofibers. Especially for o–PDA, the resulting PANi nanofibers exhibited the largest specific capacitance of 1115.7Fg−1 at the scan rate of 5mVs−1, and 345.3Fg−1 at the specific current of 0.5Ag−1 in 1.0M H2SO4 electrolyte. However, in 0.5M Na2SO4 electrolyte, its specific capacitance decreased to 254.5 and 210.4Fg−1, whereas 834.6 and 652.5Fg−1 for PANi/PPy composites at the scan rate of 5mVs−1 and at the specific current of 0.5Ag−1, respectively. Moreover, a great improvement on cycling stability for the composites could be achieved, benefiting from the unique core–shell nanostructure and strong synergy effect between PANi and PPy.