A high-performance capillary electrophoresis with amperometric detection (CE-AD) method has been developed for the simultaneous determination of the pharmacologically active ingredients in Cynomorium songaricum in this work. Under the optimum conditions, phloridzin, epicatechin, catechin, naringenin, rutin, luteolin, quercetin, gallic acid, and protocatechuic acid can be well separated or nearly baseline separated (epicatechin and catechin peaks) within 31 min at the separation voltage of 14 kV in a 50 mmol L(-1) Borax running buffer (pH 9.0). Detection limits (S/N=3) ranged from 5.7 x 10(-8) to 8.5 x 10(-9) g mL(-1) for all nine analytes. This procedure was successfully used for the analysis and comparison of the content difference of C. songaricum samples collected from different places based on their electrophorograms or "electromigration profiles".