The anionic part of ionic liquids can provide additional interactions during chromatographic separations. In this work, the chromatographic separation performance of a silica column functionalized with 1-propyl-3-methylimidazolium chloride ionic liquid was improved by insitu anion-exchange from chloride anions to dodecyl sulfonate anions and dodecylbenzene sulfonate anions. The separation performances of these ionic liquid functionalized phases were investigated and compared with each other using polycyclic aromatic hydrocarbons, phthalates, parabens, and phenols as model compounds. Results indicated that the new columns presented a better chromatographic separation than the original one. This was ascribed retention mechanism from organic anions. The introduction of dodecyl sulfonate anions increased the hydrophobicity of stationary phase. Furthermore, the phenyl groups of dodecylbenzene sulfonate anions could provide an enhanced selectivity to aromatic compounds such as polycyclic aromatic hydrocarbons by π-π interactions. Analysis repeatability of the new columns was satisfactory (RSD of retention time, 0.10-0.40%; RSD of peak area, 0.66-0.84%).