Farsetia macrantha Blatt. & Hallb. is an endemic and critically endangered plant species of Indian Thar desert. Being an endemic and threatened plant species, there is need to develop an efficient in vitro regeneration protocol for its conservation. Since, there is no published report on in vitro regeneration of F. macrantha, therefore, present study was designed to develop an efficient micropropagation method of F. macrantha along with foliar micromorphological studies. Cotyledonary node taken from 15 to 20 days old seedlings was used as an explant for in vitro regeneration. MS medium supplemented with additives ascorbic acid (50 mg l−1), citric acid (25 mg l−1), l-arginine (25 mg l−1) and adenine sulphate (25 mg l−1) and 0.5 mg l−1 BA was best for shoot bud induction. Different types, concentrations and combinations of cytokinins (BA, Kin and mT) and auxin (IAA) tested for shoot multiplication, maximum number of shoots (25.10 ± 0.69) regenerated on MS medium containing additives and combination of two cytokinins 0.5 mg l−1 BA + 0.25 mg l−1 Kin. Microshoots were rooted successfully with highest rooting response (75.59%) on ½ MS medium containing 2.0 mg l−1 IBA. In vitro rooted plants were hardened with ~ 75% survival rate. Comparative foliar micromorphological studies conducted among in vitro grown and hardened plants suggest the developmental changes of micropropagated plants during acclimatization. The present in vitro regeneration protocol could be used for large-scale propagation and conservation of F. macrantha. Farsetia macrantha is an endemic and critically endangered plant species of Indian Thar desert and presently it is restricted only to the Barmer district of Rajasthan, India. In the present study, an in vitro regeneration method has been developed first time for its conservation.