Solanum capsicoides All. is a rare and ethnobotanically significant therapeutic plant used in many ayurvedic formulations in India to treat cough, asthma, and enteric fever. The lack of bulk availability due to urbanization and repeated clearing of domestic areas has drastically reduced the population of S. capsicoides (Dharman and Anilkumar, 2018). Hence, the present work has been undertaken to establish a reproducible protocol for the rapid multiplication of S. capsicoides via somatic embryogenesis. Plant growth regulators such as thidiazuron (TDZ), zeatin (ZEA), and gibberellic acid (GA3) in different concentrations and combinations were used for somatic embryogenesis. Cotyledon is the most suitable explant for somatic embryogenesis, and the optimum number of somatic embryos was obtained from Murashige and Skoog (MS) medium fortified with 2.27 µM TDZ. Murashige and Skoog (MS) medium supplemented with 11.4 µM ZEA and 0.29 µM GA3 resulted in the maximum germination of somatic embryos. The elongation of the shoot was successfully achieved within 30 d after transferring to 4.56 µM ZEA and 0.58 µM GA3-containing medium. Plantlets regenerated from somatic embryos showed a maximum of 90% survival rate after field transfer. Microtome sections and stereo-zoom microscopy clarified the development of different stages of somatic embryos. To study the genetic integrity of regenerated plants, inter-simple sequence repeat (ISSR) markers were used, and the low-level diversity indicated by polymorphism information content (PIC) value of 0 to 0.13 observed suggests genetic similarity among the seed germinated and regenerated plants of S. capsicoides All. This study successfully established a regeneration protocol via somatic embryogenesis in S. capsicoides. The regenerated plants were clonally identical and thus can be concluded as a well-suited method for its multiplication and conservation.