Dalbergia nigra is an endangered species from the Brazilian Atlantic Rainforest, and in vitro propagation can be applied for the conservation of this species. The aim of this study was to establish in vitro propagation and ex vitro rooting in D. nigra and evaluate the alterations in polyamines (PAs) and protein profiles during shoot development. The effect of MS and WPM culture media on in vitro germination was tested (%). For shoot induction, explants of apical and cotyledonary nodal segments from 45-day-old seedlings were inoculated in WPM culture medium supplemented with benzyladenine (BA; 0, 2.5 and 5 μM). Shoots obtained in vitro without and with 2.5 μM BA were rooted ex vitro with different concentrations (0, 100 and 500 μM) of indole-3-butyric acid (IBA). The best growth of seedlings was obtained in WPM culture medium. Treatment with 2.5 μM BA significantly increased the length of shoots by increasing free putrescine contents and the accumulation of proteins associated with shoot elongation, such as aspartate aminotransferase, elongation factor, calreticulin-3, and cell division cycle protein 48. Ex vitro rooting was obtained in all treatments of IBA, and the use of auxin was not necessary. The BA used for shoot multiplication significantly affected rooting, reducing the induction and number of roots but increasing the length of roots. This study showed the relevance of cytokinin, PAs and proteomic profiles on in vitro shoot development, as well as the auxin and cytokinin balance on ex vitro rooting in D. nigra.