Shan-dou-gen is the dried roots of Sophora subprostata (Leguminosae) and a commonly used Chinese herbal drug in Taiwan. It possesses antipyretic, anti-inflammatory, analgesic effects and is used to treat sore throat and acute pharyngolaryngeal infections. To evaluate the quality of S. subprostata, a simple, rapid and accurate high-performance capillary electrophoresis (HPCE) method was developed for the assay of two alkaloids: matrine and oxymatrine. The electrolyte was a buffer solution containing 75% 130 mM phosphate buffer (NaH 2PO 4/H 3PO 4, pH 3.5) and 25% acetonitrile. Applied voltage was 10 kV and temperature was 30 °C. 2-(4-Hydroxyphenyl)ethylammonium chloride was used as an internal standard and detector set at 200 nm. The contents of matrine and oxymatrine of S. subprostata in several different samples of crude drugs and commercial concentrated preparation have also been determined.