This study demonstrated that somatic embryogenesis and de novo shoot organogenesis-based systems of root-derived Lisianthus (Eustoma grandiflorum) explants can be alternatively induced by exogenous supply of auxin or cytokinin. Somatic embryogenesis was observed when root explants were cultured in the dark on Murashige and Skoog-based medium supplemented with 10 μM 2,4-dichlorophenoxyacetic acid (2,4-D). Somatic embryos were differentiated by transferring embryonic calluses to an embryo conversion phase medium containing 2 μM 6-benzyladenine (BA) to promote full plantlet development. Regarding de novo shoot organogenesis, the addition of 4 μM of either BA or zeatin was the most effective treatment for inducing adventitious shoot buds. A detailed histological characterization of somatic embryogenesis and de novo shoot organogenesis showed that both morphogenetic processes shared the same cellular origin. The formation of somatic embryos and adventitious shoot buds occurred through the reactivation of pericycle and vascular parenchyma cells into proembryos and meristemoids, respectively, which consisted of meristematic cells with similar characteristics. These results provide further evidence of optimization of in vitro propagation as a useful approach to improve this important ornamental species.