Objective:To establish a method for the determination of five primary alkaloids (Berberine,Palmatine, Jatrorrhizine,Evodiamine and Rutaecarpine)in the Mixture of Rhizoma Coptidis and Fructus Evodiae by micellar electrophokinectic chromatography.Method:The separation was performed on a fused-silica capillary of 75 μm× 74 cm(65 cm effective length).20 mmol·L~(-1)phosphate buffer(including 50 mmol·L~(-1)SDS,pH 6.9)-acetoni- trile(8:5)was selected for the running buffer.The voltage applied was 25 kV.The sample was injected by air pres- sure (2 kPa,3 s).The detection wavelength was set at 225 nm.Results:The regression equations for Berberine,Pal- matine,Jatrorrhizine,Evodiamine and Rutaecarpine showed good linearity in the ranges of 0.027-1.345,0.018- 0.710,0.018-0.712,0.016-0.653 and 0.016-0.661 mg·mL~(-1) respectively.The recoveries (n=6) were 99.2%(RSD 3.2%),103.1%(RSD 2.1%),100.9%(RSD 1.5%),99.4%(RSD 2.9%),101.9%(RSD 3.3%),respectively.Five alkaloids in Rhizoma Coptidis,Frectus Evodiae and the Mixture of Rhizoma Coptidis and Fructus Evodiae were determinated.Conclusion:The method is simple and accurate.It can be applied to optimize the extraction process and quality control of the Mixture of Rhizoma Coptidis and Fructus Evodiae.