Aqueous extract of freshwater mussel, Lamellidens marginalis is known to possess potent antioxidant and anti-inflammatory activity. Here, we have made an attempt to purify anti-inflammatory protein from Lamellidens marginalis extract (LME). Aqueous LME was prepared, and total protein was precipitated by 60% ammonium sulfate followed by purification through ion exchange chromatography. Isolated fractions were studied for anti-inflammatory activity in in vitro and in vivo experimental models. Active fractions were characterized by SDS PAGE and HPLC. Protein recovered from ammonium sulfate precipitation showed four distinct peaks in diethyl-aminoethyl cellulose ion exchange chromatography when eluted with stepwise salt gradient. Protein fraction eluted in 0.5 M sodium chloride solution showed maximum specific activity and anti-inflammatory activity in acute model and adjuvant induced chronic inflammation model. This fraction also showed cyclo-oxygenase 2 (COX2) enzyme inhibitory activity in in-vitro system. In SDS-PAGE 0.5 M NaCl fraction showed multiple bands after Coomassie brilliant blue staining and three distinct peaks in HPLC. In this study, we identified an anti-inflammatory protein fraction with high anionic property which could be attributed to inhibition of COX2 enzyme activity.