Vannamei shrimp culture in intensive and traditional ponds is developing rapidly in Indonesia. The development starts with technology, high density, and feeding systems. It results in very high organic material produced in the aquaculture ponds, and this water quality management is necessarily maintained. This study aims to isolate and identify the molecular of proteolytic bacteria from Vannamei shrimp aquaculture ponds using a different system that is as probiotic agents. This study used a survey method and random sampling technique from traditional and intensive shrimp aquaculture. The results showed that the proportion of proteolytic bacteria in traditional ponds was higher than that in intensive ponds. The screening based on colony morphology and highest activity index obtained 4 bacterial isolates of Vibrio sp. and Pseudoalteromonas white an identity value of 98.23-99.80%. The value of this activity was observed at 7.0 cm, subsequently inhibiting Vibrio sp. by 1.5 cm. The bacteria were also found to develop at pH 7 and a temperature of 28°C adequately. Additionally, the maximum proteolytic activity at a 48-hours incubation indicated their potential relevance as a biotechnological probiotic. Further studies on the potential of Pseudoalteromonas ganghwensis strains found that the bacteria have antimicrobial activity and are sensitive to antibiotics that can be used as aquaculture probiotic agents.