Under each of 38 buffer conditions, six migration parameters of 14 flavonoids were obtained in capillary zone electrophoresis (CZE) and nine parameters in micellar electrokinetic capillary chromatography (MEKC). A total of 183 structural descriptors for each flavonoid were calculated to represent the molecular structures in a quantitative way. The relationship between the structural descriptors and the migration parameters of flavonoids in CZE or MEKC were evaluated by cluster and factor analyses.