Boswellia serrata is an important source of medicinal oleo-gum resins and boswellic acid, a unique non-steroidal anti-inflammatory, anti-arthritis drug. This experimental study describes the first time and in vitro direct somatic embryogenesis protocol and plantlet formation from immature zygotic embryos of B. serrata. The morphogenic potential of zygotic embryo was tested on MS medium fortified with cytokinins: 6-furfurylaminopurine [kinetin], N6-benzyladenine [BA], 1-Phenyl-3-(1,2,3-thiadiazol-5-yl)-urea [TDZ], auxins: IAA [Indole-3-acetic acid], NAA [α-naphthaleneacetic acid] and 2,4-D [2,4-dichlorophenoxyacetic acid] alone and in combination. MS medium containing 1mg/l TDZ + 0.50 mg/l 2,4-D + 200 mg/l PVP was effective for inducing direct somatic embryo in 89.63% of cultures. On the surface of the zygotic embryo observed, the globular, heart and cotyledonary stages of somatic embryo development. Better germination and conversion to plantlets (73.2 ± 1.6%) of somatic embryos were observed on subculture to GA3 alone containing medium. The survival of plantlets under ex-vitro conditions was about 72%. Flow cytometry (FCM) confirmed the stable ploidy level in regenerated plantlets. In leaf samples of somatic embryo-derived plantlets, boswellic acid isomers are detected by using UPLC-UV-MS analysis and the content of isomer 3-O-acetyl-11-keto-β-Boswellic acid (AKBA) was 0.13 µg/gm dry weights. The propagation protocol described here provides an important micropropagation technique for this valued plant. Nevertheless, this described propagation method can be used for genetic transformation and medicinally important bioactive boswellic acid production.