Dactylorhiza hatagirea, commonly known as Salam Panja, is a high-altitude medicinal herb in the Himalayan region. The species is cultivated primarily for economic purposes for its highly medicinal tubers; these are used in preparation of Salep. Its overexploitation for medicinal use and habitat destruction has led to its endangered status. Presently, an attempt was made to culture its shoot meristems (0.3-0.5 cm long) on half-strength modified Murrashige and Skoog (1962) medium with a view to conserving D. hatagirea. The growth hormones in selected nutritional combinations (IAA + BAP, NAA + KN, IBA + KN, and IBA + BAP; 1.5 mgL(- 1) each) were found to be most effective for inducing regeneration response (100%) and subsequent development of plantlets at significance p < 0.05. The combination <1/2>MS + IAA + BAP significantly advanced regeneration response (6.18 +/- 0.94(a) days), (1/2 MS + NAA + KN) significantly improved multiplication of regenerants (7.75 +/- 0.62(f)) and (1/2 MS + IBA + BAP significantly advanced healthy plantlets formation (35.53 +/- 0.62(b) days). Genetic fidelity analysis was done utilising SCoT markers to evaluate the stability of regenerated plantlets. Thirteen SCoT primers amplified 58 scorable amplicons with 77.59% monomorphism. The markers SCoT 8, SCoT 24, SCoT 26, SCoT 28, and SCoT 31 showed 100% monomorphism revealing genetic homogeneity among the regenerated plantlets. The plantlets showed 65% survival rate during ex-vitro transfer to the natural conditions. These findings provide valuable insights for in vitro propagation and conservation of this medicinally important terrestrial orchid will help in decreasing the pressure of overexploitation from natural habitats.