Heparin was isolated from Mercenaria mercenaria by ion-exchange chromatography and was fractionated into two distinct populations with immobilized antithrombin. The high-affinity glycosaminoglycan accelerated dramatically the inhibition of purified human factors IIa and Xa via purified human antithrombin. Specific anti-factor IIa and anti-factor Xa activities were 363 and 348 U.S.P. units/mg, respectively. The highly active clam heparin exhibited a molecular weight of approximately 18,000 and contained approximately 2.5 sulfate groups per disaccharide. The intrinsic fluorescence of purified human antithrombin was enhanced in the presence of the high-affinity invertebrate glycosaminoglycan to an extent comparable to the level induced by vertebrate heparin. In addition, the critical tetrasaccharides containing 3-O-sulfated glucosamine residues, which constitute part of the unique antithrombin-binding domain of mammalian heparin, were also detected in high-affinity Mercenaria heparin.