Epiphytic bacteria of macroalgae have been reported to have main role in survival by producing inhibitory components against other potential harmful or pathogenic effects. This study was conducted to access the isolation, production and purification of alkaline protease enzyme isolated from the brown algae. These seaweeds collected from Thirumallavaram, Kollam (DT) and Kerala. Among the seaweeds only Sargassum spp. and Padina spp. were most potent. Bacterial isolation and identification were performed by standard biochemical characterization. Mostly, bacteria were belonging to class Bacillales. Protease enzyme was used in a food and therapeutic enzymes applications. In this study protease was isolated and partially purified. Before the partial purification of alkaline protease enzyme was characterized against different concentrations of pH, Temperature, NaCl tolerance of some selective isolates of Bacillus spp. Compare than Padina spp. associated Bacillus only Sargassum spp. associated Bacillus were showed the screening of higher production activity and eminence characters of partial purified enzyme.