Somatic embryogenesis (SE) is a complex, multifactorial model of molecular, biochemical, physiological and developmental steps of plant embryogenesis. This regenerative route arises from a single totipotent somatic cell that has dedifferentiated or redifferentiated into an embryonic state. Additionally, it comprises a high performance in vitro regenerative system for both the mass clonal propagation of an elite genotype and/or the mass propagation of endangered plant germplasm. Following coordinated subsequent cell divisions, changes in cellular contents and balances of protein, hormones, polyamines, polysaccharides, and lipids, histodifferentiation processes takes place, culminating with the full development of a mature somatic embryo, mimicking the developmental stages observed in a zygotic embryo. These dynamics are simultaneously affected by a myriad of factors, mainly associated to epigenetic reprogramming, tissue culture environment, culture media composition, and type, levels and balances of plant growth regulators. In this context, in the present review we present and discuss three SE systems of selected and typical Brazilian native woody species, representing different taxonomic groups: Araucaria angustifolia (Araucariaceae), Acca sellowiana (Myrtaceae) and Bactris gasipaes (Arecaceae). Our approach to SE wants to contribute to the better understanding of plant cell totipotentiality, as well as to address its application in capturing genetic gains from elite genotypes, and for use in conservation programs of endangered species.