Abstract: This paper studied on purification and physicochemical characteristics of glycosaminoglycan from Pinctada martensii.The separation of the samples was identified by agarose gel electrophoresis and analyzed by infrared spectroscopy. After glycosaminoglycan was achieved from the whole viscera of Pinctada martensii via enzymatic hydrolysis by pancreatin and neutral protease of Bacillus subtilis,the crude glycosaminoglycan was purified by DEAE-52 ion exchange column with 0.5 mol / L Na Ac( p H = 6.0) and 1.5 mol / L Na Cl,then the purified product of glycosaminoglycan( GAG1 and GAG2) were obtained. The physicochemical properties of the purified product were analyzed by the method of phenol- sulfuric acid,Bradford,Orcinol,Wagner,Infrared spectroscopy.The results showed that GAG1 was heparin sodium and GAG2 was chondroitin sulfate.