Centrifugal partition chromatography (CPC) coupled online with high-performance liquid chromatography (HPLC) with diode-array detection (DAD) and mass spectrometry (MS) is presented in this work. This strategy offers the possibility to obtain simultaneously CPC fractionation of natural extracts, the HPLC fingerprint of separated fractions and structural information on molecules contained in each fraction. This new approach was applied to the fractionation and purification of xanthones from Garcinia mangostana (Clusiaceae) pericarp. A biphasic solvent system of heptane/ethyl acetate/methanol/water (2:1:2:1, v/v) was used for the CPC separation of 175 mg crude ethanolic extract. The HPLC analysis was conducted with a reversed-phase monolithic column allowing fast and repeatable separation. This combined CPC-HPLC-DAD-MS method led to isolation of 33 mg α-mangostin and 6 mg γ-mangostin at 98% and 98.5% purity, respectively, in 140 min. Furthermore, in the same time a total of 16 other xanthones were detected in the extract, and ten of them were identified on the basis of their UV and MS spectra.