AbstractMicellar electrokinetic electrophoresis was employed to determine two active components, gentiopicroside (GE) and swertiamarin (SW) in one Tibetan preparation medicine named shiweilongdankeli, two Tibetan herbal medicines named Gentiana rhodantha and Gentiana kitag and three other Chinese Gentiana medicines named Gentiana scabra, Gentiana rigescens and Gentiana macrophylla. The dissociation constants of gentiopicroside and swertiamarin determined by MEKC were 7.71 and 6.25. The optimum buffer system was 70 mm borate–10 mm sodium dodecylsulfate (SDS) –6% (v/v) ispropanol (pH 9.0). The voltage was 15 kV and detection was at 254 nm. The lower limits of detection (defined as a signal‐to‐noise ratio of about 3) were approximately 3.86 mg L−1 for GE and 5.88 mg L−1 for SW. The relative standard deviation of the migration time and peak area of the GE and SW were 2.33, 2.47 and 1.27, 2.19%, respectively and the recoveries of the two compounds were 96–104% for GE and 92–102% for SW. Copyright © 2003 John Wiley & Sons, Ltd.