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Emodin and quinalizarin were obtained by separation and purification with silica gel column chromatography and preparative high performance liquid chromatography from Aspergillus.ochraceus. The best condition of preparative high performance liquid chromatography was mobile phase, methanol: water (60: 40, V/V); the flow rate, 60 mL/min; sample mass in injection volume, 0.6g (10mL); the detective wavelength, 254nm. Purity of emodin and quinalizarin which were determined by HPLC got up to 96.8% and 95.9%. The structures of emodin and quinalizarin were analyzed by methods such as UV, IR, MS, MS/MS, NMR (1H-NMR, 13C-NMR, DEPT). Emodin and quinalizarin were found from Aspergillus.ochraceus at first time. The yield of emodin from fermentation exceeded to that obtained from Chinese traditional medicinal herbs.