Two capillary zone electrophoretic methods were developed for the routine separation of flavonoids and phenolic antioxidative compounds. The analyses were optimized for reference compounds at pH values of 7.00 and 8.85, using a 30 mM mixture of sodium dihydrogen phosphate and/or disodium hydrogen phosphate as the electrolyte solution. Analytes were detected on-column with UV absorption at 220 nm. The methods were optimized using reference compounds, with the aim of obtaining good resolution of flavonoids and phenolic compounds in real samples. The repeatability of the analyses was improved by using triphenyl acetic acid and benzoic acid as marker compounds for calculating the indices of the analytes. The separation method optimized at pH 7.00 was applied to the analysis of extracts from Eucommia ulmoides olive leaves and the method optimized at 8.85 was applied to an untreated Bulgarian red wine. Plant leaves were pretreated in four different ways, i.e., by conventional digestion both with boiling water and a water-methanol mixture, by Soxhlet extraction with an acetone-dichloromethane mixture and by supercritical fluid extraction with carbon dioxide by collection into acetone. The marker index technique, using organic carboxylic acids, was used to give indices for the flavonoids and phenolic compounds and for identification of the analytes. It was noticed that the reliability of peak identification was generally enhanced if the analytes migrated between the marker compounds. High relative standard deviations [R.S.D.s (%)] between the electrophoretic mobilities calculated using the absolute migration times of the analytes in samples obtained using different sample pretreatment techniques were due to the difference in ionic strengths of the analysed samples. The selectivity of the method (pH 7.00) was calculated for the plant extracts. The detection limit for all of the antioxidative compounds was 3 pmol.