The dependence of the catalytic properties of horseradish peroxidase on the structural changes of ionic liquids was investigated with two water-miscible ionic liquids, N-butyl-3-methypyridinium tetrafluoroborate ([BMPy][BF4]) and 1-butyl-3-methylimidazolium methylsulfate ([BMIM][MeSO4]), each of which shares an anion (BF4-) or a cation (BMIM+) with 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]), respectively. The oxidation of guaiacol (2-methoxyphenol) with H2O2 was used as a model reaction. In order to minimize the effect of solution viscosity on the kinetic constants of the enzymatic catalysis, the enzymatic reactions for the kinetic study were performed in water-ionic liquid mixtures containing 25% (v/v) ionic liquid at maximum. Similarly to the previously reported results for [BMIM][BF4], as the concentration of [BMPy][BF4] increased, the K-m value increased with a decrease in the k(cat) value: the K-m value increased markedly from 2.8mM in 100% water to 12.6 mM in 25% (v/v) ionic liquid, indicating that ionic liquid significantly weakens the binding affinity of guaiacol to the enzyme. On the contrary, [BMIM][MeSO4] decreased the K-m value to 1.4 mM in 25% (v/v) ionic liquid. [BMIM][MeSO4] also decreased k(cat) more than 3-folds [from 13.8 s(-1) in 100% water to 4.1 s(-1) in 25% (v/v) ionic liquid]. These results indicate that the ionic liquids interact with the enzyme at the molecular level as well as at a macroscopic thermodynamic scale. Specifically, the anionic component of the ionic liquids influenced the catalysis of horseradish peroxidase in different ways.