Humans are dependent on plants for medicines, food and raw materials. Among the many plants used, Henna plant (Lawsonia inermis) have been found to be useful, medicinally and commercially. The pigment lawsone (2-hydroxy-1,4-nathaquinone) derived from the plant is the source of Mehendi, used for dying. The plant has a vast repertoire of secondary metabolites, giving the plant medicinal properties like anticarcinogenic, anti-diabetic, anti-inflammatory, immunostimulatory and many more. This creates a huge demand pressure for the plant, which can’t be met by traditional farming. There have been reports of low propagation rate from stem cuttings and seed. So, micropropagation remains the only tool, for the large scale vegetative propagation, without exposing the plant to stress, saving the plant from overexploitation. The plant was established in vitro, with hormonal manipulation. The study shows BAP 4 mg/L and combination hormone of BAP 2 mg/L + Kn 2 mg/L to have best results for shoot bud multiplication. Rooting was seen to be significant in MS medium, highlighting the low cost of maintenance of the plant. Karyotype analysis was performed between in vivo and in vitro plant sets, followed by transcriptome analysis. Karyotype analysis, performed to validate the homogeneity between in vivo and in vitro plants, showed a chromosome number of 30. Transcriptome analysis through the TRAPID platform showed significant difference between in vivo and in vitro plant’s transcript sets. Pathway analysis revealed enriched secondary metabolite pathways of commercial and economic importance in the in vitro generated plantlets as compared to the wild type control.