Biotechnological tools have a large potential in breeding and biodiversity conservation programs for woody species. The use of plant cell tissue and organ cultures has emerged as an important tool, when the propagation of tropical woody plants in the reforestation programs is considered. This technique has been adopted for plants in which the massive propagation and ex situ conservation has been precluded by low productivity and or low viability of seeds, long-term seed maturation and limited vegetative propagation. In this regard, somatic embryogenesis (SE) has been successfully applied in production of somatic cell and viable embryos, in a morphogenetic process closely related to the natural process of zygotic embryogenesis. In addition, SE can be associated with others techniques, such as cryopreservation and synthetic seed technology, allowing the ex situ conservation of rare species or populations and the use in research to gain better understanding of biochemical, physiological, and molecular aspects of embryo development. Attempts at using SE for mass clonal propagation and ex situ conservation of elite genotypes in Brazilian pine (Araucaria angustifolia Bert O. Ktze) and Ocotea catharinensis Mez. are relatively new, and there are numerous biological unknowns regarding this complex developmental pathway. The present review is dedicated to analyze the current state of SE technology in woody plants. Some issues concerning the use of SE in A. angustifolia and O. catharinensis, including cell signaling molecules (polyamines, nitric oxide, and reactive oxygen species), establishment of molecular markers for embryogenic potential, cryopreservation and synthetic seed technology, are discussed.