This study describes preparation, characterization, application of two protic ionic liquids (PILs), Pyrrolidinium bis(trifluoromethanesulfonyl)imide ([Pyrr][TFSI]) and Diisoproyl-ethyl-ammonium bis(trifluoromethanesulfonyl)imide ([DI-PEA][TFSI]), as electrolyte for supercapacitors. Their modelisation by Density Functional Theory shows that their most evident difference is the Cosmo Volume, and the structure dissymmetry of their cation. Physicochemical and electrochemical properties are discussed according to the cation structure. Ionic conductivity increases with temperature up to 8.4 and 17.3 mS cm(-1) at 80 degrees C while viscosity decreases to 20 and 12 mPa s, at 70 C for [DIPEA][TFSI] and [Pyrr][TFSI], respectively. Ionicity was then studied using the Walden diagram, showing that they are good ILs. Their behavior was then evaluated as electrolytes for supercapacitor, on activated carbon electrodes by cyclic voltammetry, galvanostatic cycling and Electrochemical Impedance Spectroscopy. Depending on the nature of binder used in electrodes preparation, a difference of wettability was observed. [Pyrr][TFSI] displays a better diffusivity on the electrode allowing good cycling capacitance (120 F g(-1)), whereas [DIPEA][TFSI] allows higher voltage (Delta E = 2 V) and specific energy. According to the results, the cation nature is a decisive parameter on PILs electrochemical behavior for supercapacitor systems. (C) 2013 The Electrochemical Society. All rights reserved.