The potential of Capillary Electrophoresis (CE) for separation of C-Glycosylflavonoids has been examined. These compounds are found in Passiflora incarnata L. and Passiflora coerulea L. and their quantitative evaluation is the method for quality control of their extracts. Capillary zone electrophoresis (CZE) as well as micellar electrokinetic chromatography (MEKC) conditions were assayed. The optimum resolution of analytes was achieved within 12 min by using an electrolyte system of 50 mM sodium tetraborate, adjusted to pH 9.2 with NaOH and direct detection at 270 nm. Moreover, identification of several peaks was accomplished by repeating and comparing the migration times or electrophoretic mobilities and by spiking the sample solution with the pure compound prior to injection