Cryptomeria japonica (Thunb. ex L.f.) D. Don is a commercial tree native to Japan and is one of the most important forest species in that country and the Azores (Portugal). Because of the quality of C. japonica timber, several genetic improvement programs have been performed. Recently, some studies focusing on C. japonica somatic embryogenesis have been carried out. However, in this species, this process uses immature seeds as initial explants, and for this reason, it is not possible to achieve the maximum genetic gain (100% genetic of the donor plant). Although some studies have been made applying organogenesis to this species, the success of the process in adult trees is low. For this reason, our main goal was to optimize the micropropagation method by using trees older than 30 years as a source of plant material. In this sense, in a first experiment, we studied the effect of different types of initial explants and three basal culture media on shoot induction; then, two sucrose concentrations and two light treatments (LEDs versus fluorescent lights) were tested for the improvement of rooting. In a second experiment, the effects of different plant growth regulators (6-benzylaminopurine, meta-topolin, and thidiazuron) on shoot induction and the subsequent phases of the organogenesis process were analyzed. The cultures produced the highest number of shoots when QL medium (Quoirin and Lepoivre, 1977) and long basal explants (>1.5 cm) were used; the shoots obtained produced a higher number of roots when they were grown under red LED lights. Moreover, root induction was significantly higher in shoots previously induced with meta-topolin.