A capillary electrophoresis method with UV detection was developed for high sensitively determining genistein. In this method, the online acid barrage stacking was applied. Four key factors influencing the stacking efficiency were systematically optimized. Genistein can be detected within 5 rain at the concentration of 10 nmol/L, which was 300 times lower than that from conventional hydrodynamic injection. The repeatability, linear range, and limit of detection of the method were investigated with satisfactory result.