Alkaloid is an old term for vegetable alkali that covers a wide range of potent plant constituents. Alkaloids comprise the largest class of plant products and were the first chemical substances to be derived from the plants. Alkaloids are defined as naturally occurring basic plant products possessing a nitrogen atom in the hetero cyclic ring with a marked pharmacological activities. These drugs are known potential pharmacological agents. They are amazing chemicals that have given humanity a wide range of natural products that are useful in the cure of various ailments. There is an urgent need to discover new antimicrobial agents for therapeutic use, as resistance to current drugs increase in severity and extent on the passage of time. The identification of new and structurally novel natural products with antimicrobial activities and hopeful new modes of action is the only way of tackling this problem. The present study is undertaken to explore a combined chemo and bio rational strategy based on alkaloids and medicinal plants products. By targeting alkaloid containing medicinal plants, we are able to obtain structural novelty with the required bio activity more efficiently. The alkaloids are readily separable from other plant metabolites by us on account of their basicity using High Performance Thin Layer Chromatography (HPTLC) with different combinations of mobile phase. The plants screened for the study were Tinospora cordifolia commonly known as Guduchi, Withania sominifera commonly known as Ashwagandha. Presence of alkaloids was detected in Tinospora cordifolia and Withania sominifera and their antimicrobial activity was evaluated against Bacillus subtilis, Staphylococcus aureus, Proteus vulgaris, Salmonella typhi, Escherichia coli, yeast Candida albicans and fungi Aspergillus fumigates, when varied and satisfactory results were obtained. Considerable activity was observed against gram positive bacteria, but not against gram negative bacteria.