A capillary electrophoresis method was developed for the simultaneous determination of five flavonoids such as luteolin-7- O-glucoside, isorhamnetin, apigenin, luteolin and quercetin in Lamiophlomis rotata (Benth.) Kudo. Optimal conditions were obtained at pH 9.0 with 30 mM borate as buffer containing 8% (v/v) acetonitrile, 20 kV as driving voltage and 210 nm as detection wavelength. The association constant K and the change in Gibbs free energy (Δ G) of the interaction of flavonoids with borate anion ion (a typical ion-dipole or ion-induced dipole interaction) were calculated for the quantitative evaluation and characterization of the interaction. The described method was successfully applied for the rapid and efficient quality control by quantifying flavonoids in L. rotata. Repeatability tests showed that the R.S.D.s of both intra- and inter-day migration times and peak areas were less than 5%. The LOD of the five flavonoids was less than 3.75 mg/l. Recovery results ranged from 94.2% to 105.1%.