The density, viscosity, conductivity, and heat capacity of 1-hexyl-3-methylimidazolium hexafluorophosphate ([C(6)mim] [PF6]) and 1-hexyl-3-methylimidazolium tris(perfluoroalkyl)trifluorophosphate ([C(6)mim][(C2F5)(3)PF3]) were measured in the (293.15 to 343.15) K range. According to these experimental and estimated results, the coefficients of thermal expansion and conductivity apparently increase from [C(6)mim][PF6] to [C(6)mim][(C2F5)(3)PF3], while the crystal energy, the temperature dependence of the heat capacity, and viscosity greatly decrease from [C(6)mim][PF6] to [C(6)mim][(C2F5)(3)PF3] in the examined temperature range. These comparisons were combined to assess the effect of the replacement of three F atoms of the hexafluorophosphate anion by three hydrophobic C2F5-groups on the physicochemical properties of [C(6)mim][PF6] and [C(6)mim][(C2F5)(3)PF3].