The present investigation evaluates the suitability of different matrices such as calcium alginate, polyacrylamide, agar-agar and gelatin for production of alkaline protease from Bacillus subtilis. Isolated from fermented fish using immobilisation approach. Calcium alginate was found to be an effective and suitable matrix for higher alkaline protease productivity compared to other matrices studied. All the matrices were selected for repeated batch fermentation. The average protease production with calcium alginate was 585 U/ml which is 70% higher production over the convention free cell fermentation. Similarly, the protease production by repeated batch fermentation was 380 U/ml with polyacrylamide, 498 U/ml with agar-agar and 438 U/ml with gelatin respectively..