Abstract The migration behavior and selectivity of thirteen sulfonamides in capillary electrophoresis (CE), with emphasis on micellar electrokinetic chromatography (MEKC) were systematically investigated using a phosphate–borate buffer electrolyte, with sodium dodecyl sulfate (SDS) as an anionic surfactant in MEKC. The optimization strategies for the separation of sulfonamides in capillary zone electrophoresis (CZE) and in MEKC are described. The migration behavior and selectivity of sulfonamides in CZE are mainly manipulated by the pH of the buffer. The migration order of sulfonamides depends on the ratios of charge to mass (q/M2/3) and is primarily determined by their pKa values. Thus precise optimization of buffer pH is crucial to further improve the separation of some closely migrating sulfonamides. On the other hand, buffer pH and micelle concentration greatly affect the migration and selectivity of sulfonamides in MEKC. The migration order of sulfonamides is mainly determined by their pKa values and the magnitude of the binding constants of solutes-to-micelles. The influences of buffer pH and micelle concentration correlate with each other. The magnitude of the binding constants correlates with the differences between the electrophoretic mobility of sulfonamides measured at a pH below pKa−2 in CZE and that in MEKC. In this work, acid dissociation constants of these sulfonamides and binding constants of sulfonamides to SDS micelles in a phosphate–borate buffer are reported.