To exploit the potential application of the conductive polymers in incorporating with carbon-based materials, polypyrrole (PPY) nanotube and polyaniline (PANI) nanofiber were synthesized and the electrochemical properties were compared. The morphology, texture and chemical structure of PPY and PANI were tested employing SEM, TEM, FTIR and XPS. The results of electrochemical tests demonstrate that the specific capacitance of PPY nanotube is as high as 463 F/g at a current density of 0.3 A/g, much higher than that of PANI nanofiber (243 F/g). Furthermore, at a current density of 0.8 A/g, the capacitance of PPY nanotube is 172 F/g, higher than that of PANI nanofiber (104 F/g). Additionally, after the long-term charge-discharge test at a current density of 1.5 A/g, the preserved capacitance of PPY nanotube is still higher than that of PANI nanofiber (106.5 F/g vs. 75 F/g). The EIS measurement illustrates that the PPY nanotube shows lower contact interface resistance and shorter ion diffusion path than the PANI nanofiber. It suggests that the PPY nanotube is a promising material to be applied in supercapacitor rather than the PANI nanofiber, because of its extended internal cavity surface area and pore volume.