Commiphora wightii is an endangered tree valued for its gum guggul-resin that has cholesterol-reducing activity is well documented in alternative systems of medicine. Phytochemical investigations were taken up in six accessions of C. wightii and micropropagation protocol developed for its conservation. The leaves and gum of C. wightii were qualitatively and quantitatively tested for secondary metabolites and an elite accession with very high contents of total sterols and phenols was identified. An efficient HPLC method was utilized in the present study to estimate the valuable and pharmaceutically important steroid compounds present in its gum, viz. E-Guggulsterone and Z-Guggulsterone, which are hypolipidemic agents. The estimation resulted in the values of 2.45 mg/L and 2.17 mg/L for E- and Z -guggulsterone respectively. A highly efficient micropropagation protocol with good rooting and a high plantlet survival was developed from the nodal explants to aid its conservation and 360 plants survived out of 396 plants (transferred to the field) with a high percentage of survival (92.8%). The micropropagation efficiency reported presently in C. wightii far exceeds all the earlier reports and was mainly achieved due to strong rooting and healthier state of plantlets.