In the present study, total seven bacterial isolates were obtained from the mangrove sediment. Out of seven isolates, MS2 showed larger clear zone on fibrin place, which indicates the presence of nattokinase enzyme. The thrombolytic effect of nattokinase enzyme obtained from Bacillus sp. of the the mangrove sediment was studied in vitro. The enzyme (10µl) obtained from this strain showed fibrinolytic activity on casein agar plate. At 300µl concentration, this enzyme showed thrombolytiv activity (> 50%) blood clot lysis. The enzyme showed optimum stability at 500C. for 30 minutes. The results showed that Nattokinase from Bacillus sp. played a significant role in thrombolysis and anticoagulation in vitro. The phylogenetic analysis identified the enzyme producing strain as Bacillus sp. The results indicate that the pure enzyme has a potential in dissolving blood clot, and the possibility for application in the treatment of thrombosis.