The catalytic hydrogenation of 1,3-cyclohexadiene using [Rh(COD)(PPh3)(2)]NTf2 (COD = 1,5-cyclooctadiene) was performed in two ionic liquids: 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide, [C(1)C(4)Im][NTf2], and 1-butyl-2,3-dimethylimidazolium bis(trifluoromethylsulfonyl)imide, [C(1)C(1)C(4)Im][NTf2]. It is observed that the reaction is twice as fast in [C(1)C(4)Im][NTf2] than in [C(1)C(1)C(4)Im][NTf2]. To explain the difference in reactivity, molecular interactions and the microscopic structure of ionic liquid +1,3-cyclohexadiene mixtures were studied by NMR and titration calorimetry experiments, and by molecular simulation in the liquid phase. Diffusivity and viscosity measurements allowed the characterization of mass transport in the reaction media. We could conclude that the diffusivity of 1,3-cyclohexadiene is 1.9 times higher in [C(1)C(4)Im][NTf2] than in [C(1)C(1)C(4)Im][NTf2] and that this difference could explain the lower reactivity observed in [C(1)C(1)C(4)Im][NTf2].