The oleo-gum resin of Commiphora wightii (Arn.) Bhandari, a pharmacologically important balsamiferous woody shrub, has been used in treating various ailments and disorders since ancient times (2000 B.C.) due to the presence of steroidal compound guggulsterone. Two bioactive isomers of guggulsterone, E and Z, are responsible for lipid- and cholesterol-lowering and anti-cancerous activities. Further, guggul has been approved as food supplement by US-FDA as well as Council of Europe. Indiscriminate harvest of C. wightii from wild with negligible conservation efforts has lead to its inclusion in IUCN assemblage of endangered plant species. For identification of high guggulsterone yielding ecotypes of C. wightii, using high-performance thin-layer chromatographic (HPTLC) analysis, stem samples were collected from 50 plants from eleven locations in arid tracts of Haryana, Gujarat and Rajasthan. Dried, powdered material was subjected to extraction with petroleum ether using soxhlet apparatus. Samples were spotted on precoated activated silica plates (60F-254) and were developed using toluene–acetone (9:1 v/v) as mobile phase. The analysis was carried out in the absorbance mode at 250 nm using HPTLC scanner. The regression analysis data for the calibration plots for E and Z guggulsterone showed good linear relationship with R2 = 1 and 0.9897, respectively. Highest concentration of guggulsterone E (284 μg/g dry wt) was found in the accession collected from Palana, Bikaner whereas highest guggulsterone Z concentration (89.5 μg/g dry wt) was found in the accession collected from CAZRI, Jodhpur.