Musa balbisiana (BB) and M. acuminata (AA) are the two wild diploid progenitors of the cultivated, triploid, tetraploids bananas and plantains. Collection and safe conservation of crop wild relatives (CWR) has gained tremendous importance, as they are the reservoir of genes and traits required to combat climate change effects and the emerging biotic and abiotic stresses. The purpose of this study was to investigate seed storage behavior of M. balbisiana for devising and applying suitable strategies to conserve CWR of banana/plantain germplasm in gene banks, both for short-and long-term. Seeds (from mature fruits) of three accessions of M. balbisiana from Field Gene Bank of ICAR-NBPGR, New Delhi (EC653579) and natural populations from ICAR-NBPGR, Thrissur, Kerala (IC630992) and Mizoram University, Mizoram (IC633382) were augmented and desiccated to various moisture contents (MC at 5,10,15, 20 and 25 % on fresh weight basis). Fresh and desiccated seeds were stored at three temperatures (25, -20 and -196 °C) to assess freezing sensitivity. Whole seeds as well as excised zygotic embryos were cryopreserved at the optimized MC using simple air dehydration technique. For recovery, data on in vitro regeneration of zygotic embryos was recorded and analyzed statistically to determine optimal explant and conservation regime. Whole seeds in general were difficult to germinate whereas in vitro regeneration of zygotic embryos yielded high results (95 ± 5 %). Seeds were found to be desiccation tolerant (viable up to 5 % MC) and desiccated seeds (5–10 %) were insensitive to ultra-low temperature (-20 and -196 °C), without significant loss of viability and germination potential. High moisture content (15, 20 and 25 %) in seeds led to low regeneration potential (≤50 %) due to cold injury of cells at ultra-low temperatures (-20 and -196 °C). No significant differences were observed in regeneration of fresh and cryopreserved desiccated (5–10 % MC) excised embryos (90 ± 10 %). Our studies confirm that M. balbisiana seeds are ‘orthodox’ in storage behavior, and can be easily conserved for short-term at 25 °C, medium-term at -20 °C and long-term at -196 °C with 5–10 % MC. However, unlike other typical orthodox seeds, regeneration of conserved seeds is only feasible through zygotic embryo culture under in vitro conditions, as desiccated whole seeds fail to germinate using standard protocols. For cryobanking, whole seed or excised zygotic embryo cryopreservation is a feasible option for germplasm conservation of M. balbisiana.