Aquaculture health management demands a constant growth in the production by stabilizing economic loss and implementing various natural plant-based bio products for treating pathogenic bacteria. Pathogenic effects of the Citrobacter freundii isolated from fingerlings of Tilapia collected from a fish farm showed symptoms like tail necrosis, septicemia, hemorrhage, and reddening of the body. Antibacterial activity of C. freundii was tested against various medicinal plants. Of the three plants screened, Azadirachta indica (Neem) showed good antibacterial activity against C. freundii. The present study revealed that A. indica plant extract at a concentration of 150. mg/l in vivo can be used as an alternative to antibiotics for treating this bacterial infection. The use of medicinal plant extract-mediated treatment was found to be very effective in controlling this bacterial infection. © 2014 Elsevier B.V.