The glycosaminoglycan (GAG) heparin is a polyanionic sulfated polysaccharide most recognized for its anticoagulant activity. In the present study, the GAGs were extracted from bivalve mollusc Amussium pleuronectus. The crude GAGs were fractionated by ion-exchange (DEAE-cellulose and Amberlite IRA-900 & 120) chromatography. The recovered active fractions (as determined by metachromatic assay) were confirmed by agarose gel electrophoresis and the active fractions were purified in Sephadex G-100 column. Fractionated and purified GAG molecular weight was determined through gradient polyacrylamide gel electrophoresis. The structural characterization of low molecular weight GAG was analyzed by Fourier transform infrared spectroscopy. The activated partial thromboplastin time of purified GAG is 95 IU/mg and has molecular weight 6,500-7,500 Da. The disaccharide compositional analysis on the GAG sample was sulfated like porcine intestinal mucosal heparan sulfate, and it contains equivalent amount of uronic acid and hexosamine. The results of this study suggest that the GAG from A. pleuronectus could be an alternative source of heparin.