Heparin is an attractive sulfated polysaccharide due its capacity to intefere in numerous important biological activities, such as anticoagulant and antithrombotic properties. The presence of compounds heparin-like with notable anticoagulant activity has been described in many species of invertebrates. In this work we report the fine characterization of an unusual heparin purified from the viscera (heads) of the shrimp Litopenaeus vannamei, a marine invertebrate which represents one of the main products of Brazil's exportations. The heparin-like compounds was isolated after proteolysis and fractionation by ion exchange resin and purified by DEAE-Shephacell. Structural analysis of shrimp heparin, performed by its enzymatic depolimerization as well as mono- and two-dimensional nuclear magnetic resonance (NMR) spectroscopy revealed that shrimp heparin is enriched with glucuronic acid residues and rare 3-O-sulfated glucosamine residue, a typical marker for the pentasaccharide sequence that is essential for heparin-binding properties to antithrombin (AT) and responsible by its anticoagulant activity and that has not previously been found in crustacean heparin. A shrimp heparin fraction of high affinity for AT was also fully characterised by NMR.  Taken together, the results show that shrimp heparin has a peculiar structure, due its higher amount of 3-O-sulfated glucosamine residues (14%) when compared to mammalian heparins (7%). Beside theses differences, it was observed for shrimp heparin a higher molecular weight (36 KDa) and a lower anticoagulant activity (90 UI/mg).  These novel natural products from invertebrates can serve in future as an alternative source for the heparin production or could be used as a model to elucidate biological and pharmacological interactions.