Traditional medicine dating back to centuries ago has been used to treat several ailments of humans. Berberine is a chemical compound that is found in plants which is being used in the form of drugs to work against various diseases. For optimum production of Berberine suitable plant species must be selected out of Coptis japonica and Argemona mexicana which are high yielding. From the pathway of Berberine production it is known that more the amount of substrate Canadine gives more amount of Berberine. The objective of this work is to compare the Canadine production efficiency among Coptis japonica and Argemona mexicana by molecular level studies for both the species. It is concluded that the enzyme, (S)-canadine synthase from Argemona mexicana is more efficient towards the production of (S)-canadine which in turn lead to Berberine production. Later the efficiency of Berberine against various disease targets is tested by molecular docking approach under same experimental conditions. Molecular docking results conferred the efficiency of Berberine in the treatment of gastric cancer over the other diseases.