Gradient centrifugal partition chromatography (GCPC) method was developed and applied to isolate 3,5-dimethoxyphenanthrene-2,7-diol (DMP) and batatasin-I (BA-I) from the dichloromethane soluble extract of Dioscorea opposita. In this method, the lower phase of n-hexane-methanol-water system (HMW, 10:9:1, v/v) was used as a mobile phase A (MpA) and water was used as a mobile phase B (MpB). This gradient CPC method is comparable to that of reversed-phase HPLC method in that the stationary upper-phase of HMW (10:9:1 v/v) works as if it were reversed-phase silica gel due to its hydrophobic property, while the lower phase (MpA) and water (MpB) functioned as hydrophilic mobile phases. The initial condition of the mobile phase was 20% MpA/80% MpB and maintained for 150 min to obtain DMP (1.2 mg), and then MpA was increased up to 50% to elute BA-I (1.7 mg). The purities of DMP and BA-I were 94.1% and 98.3% with the recovery yields of 83% and 86%, respectively. Similar results were obtained by linear-gradient CPC. The CPC peak fractions were identified by comparing their retention time to those of authentic samples of DMP and BA-I and their spectroscopic data (1H NMR and 13C NMR) to those of literature values.