Cryopreservation is an important technique for the long-term storage of economically important plant germplasm. In this study, an efficient protocol was developed for the long-term conservation of seven economically important Musa taxa: M. acuminata Colla ssp. burmannica N.W. Simmonds, M. acuminata Colla ssp. zebrina (Van Houtte) R.E. Nasution, M. balbisiana Colla, M. basjoo Sieb., M. ornata W. Roxburgh (St. Lavender), M. velutina H. Wendl. et Drude (Velvet Pink Banana), and M. acuminata’ balbisiana. The seeds were dehydrated in a sterile laminar flow cabinet for different exposure times and then they were directly immersed in liquid nitrogen. The critical point was to support the initial germination of cryopreserved seeds and this was achieved by the excision of zygotic embryos after liquid nitrogen treatment that allowed the seed germination. The best moisture content for tolerance to cryopreservation ranged from 15.8% (M. acuminata ssp. zebrina) to 17.1% (M. ornata) and the maximum post-cryopreservation germination rates varied from 86.4% (M. velutina) to 55.0% (M. ornata). All seedlings derived from seeds germinated after cryopreservation were easily rooted and acclimated to greenhouse conditions.