The elution order of the hop α- and β-acids has been studied under different modes of electrokinetic separation. A model is advanced to explain the shorter migration times of the more hydrophobic β-acids compared to the α-acids in micellar electrokinetic chromatography (MEKC). For quality control of the bitter principles in hops, the ruggedness of electrokinetic separation could be improved by replacing MEKC by microemulsion electrokinetic chromatography (MEEKC).