A dermatan sulfate, similar to the mammalian glycosaminoglycans but not identical with any of them, has been isolated from the body of the ascidian Ascidia nigra. Degradation with chondroitin ABC lyase, analysis of the disaccharide products by digestion with chondro-4- and -6-sulfatases, and 1H and 13C NMR data confirm that the predominant structure is [4-alpha-L-IdoA-(2SO4)-1-->3-beta-D-GalNAc(6SO4)-1]n. Mammalian dermatan sulfate is an anticoagulant due to its ability to potentiate inhibition of thrombin by heparin cofactor II. The structure in dermatan sulfate which binds to heparin cofactor II is [4-alpha-L-IdoA-(2SO4)-1-->3-beta-D-GalNAc(4SO4)-1]n, where n > or = 3. We have compared the ascidian dermatan sulfate with mammalian dermatan sulfate and with chemically oversulfated mammalian dermatan sulfate for anticoagulant activity as measured by the activated partial thromboplastin time assay and for its ability to potentiate heparin cofactor II. In spite of its high content of 2-O-sulfated alpha-L-iduronic acid residues, the ascidian compound had no discernible anticoagulant activity and had low ability to potentiate heparin cofactor II. These results suggest that 4-O-sulfation of the N-acetyl-beta-D-galactosamine residues is essential for the anticoagulant activity of dermatan sulfate.