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The study reports a low-cost micropropagation protocol for Nardostachys jatamansi , a high value, critically endangered Himalayan herb. Shoot-bud bearing rhizome segments of the plant were made to sprout and elongate on 0.8% agar-gelled Murashige and Skoog's medium containing 3% sucrose. The sprouted shoots were then multiplied on agar-gelled as well as liquid MS medium containing various concentrations and combinations of kinetin (Kn) and 1-phenyl-3- (1,2,3-thiadiazol-5-yl) urea (thidiazuron or TDZ). Maximum number of shoots developed per explant after 30 days on 100 ml agar gelled (6.7 shoots) and 30 ml liquid (6 shoots) MS medium containing 0.5 mg l−1 Kn and 0.75 mg l−1 TDZ. Although rooting of in vitro shoots was attempted on full as well as half-strength MS medium containing different auxins, rooting was achieved in 100% shoots (3.07 roots/ shoot) after 30 days on half-strength MS medium supplemented with 1.0 mg l−1 indole-3- acetic acid (IAA). Different potting mixtures were used to acclimatize the micropropagated plantlets under polyhouse condition, but a maximum of 83% survival was recorded in sand and sand plus soil. The genetic fidelity of the in vitro plantlets was also assessed using Start Codon Targeted Polymorphism (SCoT) and Directed Amplification of Minisatellite DNA (DAMD) markers, and a total of 8.03% polymorphism was recorded. Eventually, the cost of micropropagation was reduced by 6.4 times during shoot multiplication and further by half during rooting. The present micropropagation method developed for N. jatamansi can have potential applications in medicinal plant-based industry. [Display omitted] • A low-cost micropropagation method for critically endangered Himalayan medicinal herb. • Cost of in vitro shoot multiplication reduced by 6.4 times in liquid shoot multiplication medium. • In vitro raised plants showed 8.03% polymorphism as compared to mother plant in genetic variability analysis. [ABSTRACT FROM AUTHOR]