Catfish is one of the freshwater aquaculture commodities with a high level of consumption and production in Indonesia. Disease outbreaks could occur in catfish farming activities caused by pathogenic bacteria. Several species of pathogenic bacteria can cause disease in catfish, resulting in mass death. This can lead to decrease in the food quality of freshwater fishery products, especially catfish. In cultured system, aquaculture occurrence of diseases can cause severe financial losses. Catfish samples were obtained from catfish farming with clinical symptoms of reddish spots on the outside of the body. Bacteria were isolated from the kidney and liver under aseptic conditions. These bacteria isolates were identified through their colony morphology, Gram staining, biochemical tests, molecular test, and antibacterial test of Bacillus spp. using spot and disc diffusion test. Identification based on 16S rRNA gene showed that GL1 was 99.92% closely related to Aeromonas widowei, HL1 was 100% closely to Bacillus amyloliquefaciens, and GL2 and HL2 was closely related to Bacillus cereus. The antibacterial test results of APD10 isolates of Bacillus velenzensis species inhibited GL2 pathogenic bacteria with an inhibition zone of 22.15 mm in the very strong inhibition zone and HL2 pathogenic bacteria with an inhibition zone of 8.5 mm in the moderate inhibition zone. Bacillus velezensis was isolated from the sponge Aplysina sp. could be further utilized as a biocontrol agent for the pathogenic bacteria, Bacillus cereus, that infects catfish.