Capillary electrophoresis-electrospray ionization-mass spectrometry (CE-ESI-MS) was applied to the analysis of polar positional and geometrical anionic isomers. Since the investigated positional and geometrical anionic isomers have different pK(a) values, they could be separated by CE-ESI-MS under simple analytical conditions using a bare fused-silica capillary and volatile ammonium acetate buffer after optimizing buffer pH. Ortho-, meta-, para-hydroxybenzoate positional isomers were completely separated on a fused-silica capillary with 20 mm ammonium acetate buffer at pH 10.0, and cis-, trans-cyclohexane dicarboxylate geometrical isomers could be also separated with 20 mm ammonium acetate buffer at pH 4.0. Several analytical parameters affecting ESI-MS sensitivity were also investigated. It was found that both running buffer pH and sheath liquid pH had significant effects on the selectivity and the sensitivity on CE-ESI-MS analysis while sheath flow rate and other parameters had little influence. Under optimized conditions, linearity, detection limit, and repeatability of the analysis of hydroxybenzoate isomers were examined, and good results were obtained. It was found that the method presented in this paper is a simple, robust, and cost-effective method for simultaneous analysis of positional and geometrical anionic isomers as well as of other small anionic compounds.