The present study describes the isolation, purification and structural characterization of heparan sulfate (HS) from marine scallop. Enzymatic depolymerization of the isolated HS, followed by polyacrylamide gradient gel electrophoresis (PAGE), confirmed its presence of HS is by metachromatic activity and agarose gel electrophoresis. The purity of HS is determined by the following treatment with heparin lyases though PAGE. 1H NMR spectroscopy revealed that the marine scallop HS is enriched in both glucuronic and sulfated iduronic acid residues. The result of this analysis clearly demonstrates that the isolated glycosaminoglycan (GAG) is HS. Marine scallop HS has contents of carbon, hydrogen, nitrogen and sulfated disaccharide and an elevated average sulfation level. The activated partial thromboblastin time (APTT) and prothrombin time (PT) of marine scallop HS, are lower than standard bovine intestinal HS. Moreover, marine scallop HS shows equal degree of sulfation to HS standard.