Abstract: The production of ATE(anti-thrombus enzyme) from a kind of Bacillus subtilis immobilized in NaCS-PDMDAAC microcapsules was studied.The influence of mean diameter of microcapsules, concentration of PDMDAAC and the components of culture medium on the production of ATE in the condition of encapsulation culture was studied. In shaking flasks, the maximum enzyme activity in microcapsules was 1850 UK·ml -1 when the mean diameter of microcapsules was 1.60 mm, the concentration of PDMDAAC was 2.0% and the culture medium was LB culture medium(Tryptone)+glucose(0.5%)+phosphate buffer(100 ml).A bubbling culture system was designed. In this system, the maximum enzyme activity in microcapsules was 2050 UK·ml -1 , which was 3.6 times that in the condition of suspension fermentation; the maximum cell density in microcapsules was 4.89×10 9cells·ml -1 , which was 2.7 times that in the condition of suspension fermentation.