The present investigation was carried out to study the active component of Bacillus subtilis, a gastrointestinal bacterium of mrigal (Cirrhinus mrigala) that shows inhibitory activity against a wide range of fish pathogens. The bacterium was found to inhibit all the fish pathogens and an extra cellular protein fraction (ECP) of 5-10 kD was found to be the active component responsible for inhibitory activity. The component was heat stable (60°C for 1 h) and a change in pH had no effect on the antibacterial activity. The protein fraction was sensitive to trypsin, chymotrypsin, lysozyme, and proteinase K at 2.5 mg/ml and resistant at 0.1 and 0.5 mg/ml. The present investigation confirmed that the active component of the B. subtilis responsible for antibacterial activities against common fish pathogens is a low molecular weight protein fraction (5-10 kD). A protein or peptide with such a low molecular weight has the potential to serve as an alternative health management strategy for combating disease in aquaculture