A simple and rapid method for the simultaneous determination of five anthraquinone derivatives including aloe-emodin, emodin, chrysophanol, physcoin and rhein in Rheum species and Polygonum cuspidatum was established by capillary zone electrophoresis (CZE) using beta-cyclodextrin (CD) as modifier and urea to enhance its solubility. The apparent binding constants of these derivatives with beta-CD were evaluated. After an optimization study, the best conditions were selected using 35 mM phosphate buffer (pH 11.0) containing 20 mM beta-CD and 2 M urea, applied voltage 20 kV and detection at 254 nm. Under such conditions, all of the five anthraquinones were baseline-separated within a short analysis time of 12 min with symmetrical peaks and high theoretical plate numbers (189,000-314,000). The RSD values of the migration times and peak areas were 0.6-1.1, 1.3-1.9% (intra-day) and 0.6-1.5, 1.3-2.8% (inter-day, for a 5-day period), respectively. The limits of detection for the analytes (S/N = 3) were 0.33-0.62 microg/ml. The recoveries were ranged from 93.37 to 107.69%. The proposed method was successfully applied to the determination of anthraquinones in ethanol extracts of two kinds of Rheum plants (R. palmatum and R. hotaoense) and P. cuspidatum.