The natural populations of Bacopa monnieri L., is severely affected by increased indiscriminate collection and overexploitation. There is a need to establish a micropropagation method that should perform effectively for commercial propagation and conservation. In this study, various physiological elements such as medium strength, carbon source (1% to 4%), concentration of agar (0.6%–0.9%), medium PH (5.4–6.0) was optimized for the high frequency regeneration of B. monnieri. Among different cytokinins tested, N6-benzyladenine (BA) was found to be better cytokinin over kinetin for shoot multiplication. The shoot cluster, when subcultured to its same medium, the multiplication rate of the shoot increase significantly by the end of the fifth subculture. The highest number of rooted shoots (10.75) was obtained with half-strength MS medium supplemented with 1.0 mg/l Indole-3-butyric acid (IBA). Among the experiments tested on different soil mixtures, the experience of higher survival of plants in sand, soil and compost (2:2:1) showed a condition survival rate of 87.7% in field conditions. Randomly amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) marker analysis indicated a high level of uniformity between regenerated plants and together with the mother plant. This study provides important information about selection of suitable explants, micropropagation medium and strategies to improve mass multiplication of B. monnieri which offers a scope for commercial propagation.