In this paper, selective separation of the isomeric compounds geraniol and nerol, based on the preferential affinity of -cyclodextrin (-CD) for geraniol was investigated. To demonstrate the potential application of -CD for separation of geraiol from nerol, the structure of the inclusion complexes was characterized with various physico-chemical techniques. The selective noncovalent binding property of -CD was confirmed by quantum-chemical calculations. For the mixture, which contains 50 wt% of geraniol and nerol, respectively, 96% of geraniol in complex can be obtained, and the similar separation efficiency was found after use for three times.