This study was undertaken to purify the anticoagulant polysaccharide from Pachymeniopsis elliptica. The anticoagulant compound (PE-2IVc-2-1) was isolated from the crude polysaccharide (PE-2) by the sequential steps such as ultrafiltration (PE-2IV), anion-exchange chromatography of DEAE-Toyopearl 650C(PE-2IVc), size-exclusion chromatography of Sepharose CL-6B (PE-2IVc), and HPLC Shodex OHpak column chromatography (PE-2IVc-2-1). The apparent molecular weight of purified polysaccharide (PE-2IVc-2-1) was approximately 710 kDa. It was mainly composed of galactose (48.6%) and 3,6-anhydrogalactose (44.0%) with 27.1% of sulfate residue, in addition a trace amount of xylose (3.6%), glucose (1.1%), mannose (1.1%), arabinose (0.8%) and fucose (0.8%). The IR spectrum of the polysaccharide showed the characteristic bands of S=O(1116.74 and 1143.17 $cm^{-1}$) and C-O-S (828.19 $cm^{-1}$) stretching, respectively. The anticoagulant effect of PE-2 in ex vivo was proportional to the concentration of intravenously injected dose, up to 100 mg/kg.