A simple, rapid, and accurate method for the separation and determination of physcion, chrysophanol, aloe-emodin, and emodin in Rhubarb, Juemingzi, and Chinese herbal preparations was developed by combination of flow injection-capillary zone electrophoresis for the first time. The analysis was carried out using an unmodified fused-silica capillary (75 mm x 50 microm ID x 375 microm OD, effective separation length of 48 mm) and direct ultraviolet detection at 254 nm. By a series of optimization, the sample solvent consisted of NaOH (100 mmol/L) and ACN (1:1 v/v), and a running buffer composed of 15 mmol/L sodium borate - 12.5 mmol/L sodium dihydrogen phosphate - 42% v/v ACN (pH 10.1) was applied for the separation of the four anthraquinones. The separation was rapid and highly reproducible, with complete resolution of all four compounds within 6 min. The sample throughput rate could reach up to 12 per h. The repeatability (defined as relative standard deviation) was 4.45, 4.44, 4.34, 0.61% with peak height evaluation and 1.62, 0.89, 2.49, 2.19% with peak area evaluation for physcion, chrysophanol, aloe-emodin, and emodin, respectively.