Recently, micellar electrokinetic chromatography (MEKC) has been successfully applied to the separation of electrically neutral compounds. In this study, we applied this method in order to determine simultaneously organic sulfoxide and sulfide; benzyl methyl sulfoxide (BMSO) and benzyl methyl sulfide (EMS), respectively. Dimethyl sulfoxide (DMSO) reductase from Rhodobacter sphaeroides f. sp. denitriJicans deoxygenates (S)-BMSO preferably. The MEKC method gave reliable estimates of BMSO concentration without any pretreatment, therefore, the (R)-isomer could be recovered with high enantiomeric excess by stopping the reaction at the conversion rate of 50%. Using this detection method, (R)-BMSO was recovered with good chemical and optical yields. The simple and rapid measurement by MEKC was proved to be suitable for the kinetic resolution of racemic sulfoxide by the enzymatic reaction.