The influence of the nature of two different ionic liquids, namely 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide, [C(1)C(4)Im][NTf(2)], and 1-butyl-2,3-dimethylimidazolium bis(trifluoromethylsulfonyl)imide, [C(1)C(1)C(4)Im][NTf(2)], on the catalytic hydrogenation of 1,3-cyclohexadiene with [Rh(COD)(PPh(3))(2)][NTf(2)] (COD=1,5-cyclooctadiene) was studied. Initially, the effect of different concentrations of 1,3-cyclohexadiene on the molecular interactions and on the structure in two ionic liquids was investigated by NMR and by molecular dynamic simulations. It was found that in both ionic liquids 1,3-cyclohexadiene is solvated preferentially in the lipophilic regions. Furthermore, the higher solubility of 1,3-cyclohexadiene in [C(1)C(4)Im][NTf(2)] and the smaller positive values of the excess molar enthalpy of mixing for the 1,3-cyclohexadiene + [C(1)C(4)Im][NTf(2)] system in comparison with 1,3-cyclohexadiene + [C(1)C(1)C(4)Im][NTf(2)] indicate more favorable interactions between 1,3-cydohexadiene and the C(1)C(4)Im(+) cation than with the C(1)C(1)C(4)Im(+) cation. Subsequently, diffusivity and conductivity measurements of the 1,3-cyclohexadiene + ionic liquid mixtures at different compositions allowed a characterization of mass and charge transport in the media and access to the ionicity of ionic liquids in the mixture. From the dependence of the ratio between molar conductivity and the conductivity inferred from NMR diffusion measurements, Lambda(imp)/Lambda(NMR), on concentration of 1,3-cyclohexadiene in the ionic liquid mixture, it was found that increasing the amount of 1,3-cyclohexadiene leads to a decrease in the ionicity of the medium. Finally, the reactivity of the catalytic hydrogenation of 1,3-cyclohexadiene using [Rh(COD)(PPh(3))(2)][NTf(2)] performed in [C(1)C(4)Im][NTf(2)] at different compositions of 1,3-cydohexadiene and in [C(1)C(1)C(4)Im][NTf(2)] at one composition was related linearly to the viscosity, hence the reaction rate is determined by the mass transport properties of the media.