Crinum malabaricum Lekhak & Yadav (Malabar river lily of the family Amaryllidaceae) is a critically endangered plant species and a natural source of galanthamine. Synthetic seeds production via somatic embryogenesis was adopted as in vitro conservation strategy and proliferation of Malabar river lily in this study. Murashige and Skoog's (MS) basal medium with 8.0 mg L−1 2,4-dichlorophenoxyacetic acid (2,4-D) and additives induced maximum percentage of somatic embryos (98.4%) at various stages with an average of 53.8 somatic embryos per inoculum/tri-scale explant. Histo-anatomical examinations showed that the meristematic cell layers of reduced stem (present between the scales) had the highest embryogenic capacity. The meristematic activity of the globular somatic embryos (SEs) assisted in further differentiation of distinct stages of embryogenesis. Synthetic seeds encapsulated with 2.0% sodium alginate and 100 mM calcium chloride resulted in the development of delicate beads with 92.5% post thawing germination potential after one year cold storage in dark at - 4 °C. The effect of 6-bezylaminopurine (BAP) and indole-3 acetic acid (IAA) on germination of SEs, plantlet retrieval, and shoot and root regeneration was significant as compared with combination of BAP and α-Naphthalene acetic acid (NAA). Highest 12.8 shoots per synthetic seed and 5.6 roots/ shoot were regenerated from encapsulated somatic embryos on MS medium + 2.0 mg L−1 BAP + 0.5 mg L−1 IAA + additives. This report could help in mass propagation of C. malabaricum, and could be applied for enhanced production of galanthamine using elicitors and through genetic transformations.