Micellar electrokinetic chromatography (MEKC) was used to separate twelve lignan compounds originating from Phyllanthus plants. To increase the reliability of peak identification, two micellar systems, the sodium dodecyl sulfate (SDS) and sodium deoxycholate (SDC) systems, were investigated. Because of the high lipophilicity of the lignan analytes, tetrahydrofuran was added to the SDS micellar system to increase its separating ability. In contrast to SDS system, no organic solvent was needed with SDC micelles. Both micellar systems gave a satisfactory separation within a reasonable analysis time. On considering accuracy for quantitation, the SDS method was validated and then used to determine the content of the lignans in two Phyllanthus plants. The selectivity (elution order of the lignans) was significantly different between the SDS and SDC micellar systems. Retention in SDC-MEKC seemed to be dominated by the hydrophobicity of the lignan solutes, while in SDS-MEKC, retention was greatly influenced by hydrogen bonding interactions.