Crop wild relatives have been the potential genetic resources for addressing various issues of agri-horticulture worldwide. Endemic species of such significance require urgent attention for conservation, not only for their future potential uses in modern day agriculture but also due to the roles they play in the ecosystem of their areas of origin and rather narrow distribution. In this research, various aspects of assisted regeneration viz. seed pretreatment, substrate, storage life, stage for transplanting and post-transplanting survival were studied in an endemic, threatened wild banana species (Musa sabuana syn. M. indandamanensis). This species is unique as it produces flowers that are green/ striped green in colour, fertile seeds and golden yellow pulp (indicating the presence of beta carotene). Based on germination percentage, growth parameters, seedling vigour index and seedling survival, treatment of freshly extracted seeds with 0.1% KNO3 for 24 h prior to sowing in vermicompost as substrate was recommended for mass multiplication of the species. Seed storage behaviour was studied in the species, which suggested that the species exhibits intermediate seed storage behaviour. Seed viability was reduced over time especially after three months of storage and corresponding reduction in seedling vigour index was also recorded. Based on photosynthetic pigments analysis, eight leaf stage was found to be the best for transplanting the seedlings in the field with 100% survival. This protocol would be helpful for conserving and mass multiplying an endemic wild banana for use in future breeding programmes.