Bacopa monnieri (BM) is an endangered plant with great pharmaceutical uses. This work aims to improve the protocol of mass propagation, establish a cultivation system in the newly reclaimed lands and estimate the quantitative phytochemical and fingerprint of the cultivated plants. Numerous factors affected micropropagation; i.e, MS strength, growth regulators concentrations and types of explant. The highest shoot number and growth vigor were observed on 3/4 MS strength supplemented with 0.5 mg/l BA and big cluster as an explant. The highest roots number was obtained from 2.0 mg/l IAA and 0.1%AC. The acclimatization systems significantly affected the acclimatization of B. monnieri. The culture mills system possessed the highest acclimatized number followed by pots. The cultivation distance affected plant fresh and dry weight through 80 days of cultivation, 60cm cultivation distance was the best. The fingerprint of the cultivated plants was determined through eleven RAPD and thirteen ISSR primers. The number of AF differed according to the implemented molecular marker. The RAPD primers produced 34 AF, while ISSR gave 24 AF. The RAPD and ISSR were effective to determine the BM fingerprint. The quantitative analysis using HPLC stated that the main phenolic components in the ethanol/water extract were Chlorogenic acid and Gallic acid (330.36 µg/g and 309.86 µg/g, respectively). The Quercetin concentration was 42.99 µg/g. While the main flavonoid compound was rutin with a concentration of 506.36µg/g.