Pseudomonas syringae and Xanthomonas pathovars are major phytopathogenic bacteria known to cause severe loss in quality and yield of agriculturally important crops such as paddy, tomato, soybean and sesame. Emergence of drug resistant bacterial strains, toxic effects of synthetic drugs on host crop plants and environment has led to the search for effective, safer and ecofriendly bioactive molecule for the management of plant diseases. Medicinal plant extract is considered as effective, safe, ecofriendly and least toxic to host crop plant. In this study, antibacterial activity of stem extracts of Coscinium fenestratum was evaluated against Pseudomoans syringae and Xanthomonas pathovars in vitro. Disc diffusion assay showed that P. syringae was more susceptible and X. oryzae was less susceptible. MIC of the extract against P. syringae was 2.5mg/ml and against Xanthomonas pathovars ranged between 1.25mg – 2.5mg/ml. Further, isolation and characterization of antibacterial active principle conducted using TLC-Bioautography- agar over lay method, column chromatography and by spectral analyses (UV, FT-IR, LC-PDA-MS and NMR) revealed that, antibacterial active principle as Berberine, a yellow colored, benzoisoquinoline alkaloid, known to have many bioactive potentialities. In conclusion, the plant extract/ berberine could be utilized for management of bacterial infection/s in crop plants after toxicity and field level evaluations.