The induction of somatic embryogenesis in banana is extremely difficult because of endogenous problems of the species and genotype dependency. Establishing a suitable protocol for somatic embryogenesis is necessary for applying biotechnological approaches to assist the genetic improvement, by facilitating the access to individual cells or groups of cells for use in genetic transformation, and the induction of polyploidy and mutagenesis. Embryogenic cultures were induced from immature male flowers of two important cultivars of banana, ‘Grand Naine’ (AAA) and ‘Tropical’ (AAAB), using immature male flowers. Cell suspensions were established, and regenerated plants were evaluated for their genetic stability using 11 simple sequence repeat markers. For induction of embryogenesis, different doses of autoclaved glutamine in the induction medium were used, and somatic embryos were converted into plants in medium supplemented with benzylaminopurine and naphthalene-1-acetic acid. ‘Grand Naine’ formed somatic embryos in glutamine-free media, while ‘Tropical’ somatic embryos grew in the presence of autoclaved glutamine. During regeneration, ‘Grand Naine’ showed better results for formation of embryos in culture medium without growth regulators, but these embryos were not converted into plants when kept in the same medium, while ‘Tropical’ produced a large number of plants regenerated when kept in the same medium. The simple sequence repeat markers used did not detect any genetic variation. These results suggest that the establishment of embryogenic cell suspension cultures of banana may be effective for production of genetically stable plants on a large scale as well as being a biotechnological tool to support banana genetic improvement.