Seeds are the major organs responsible for the continuation of the plant’s life cycle. The aim was to investigate the relationship of soluble sugars, polyamines and amino acids on seed germination and early seedling growth in Plathymenia foliolosa Benth. and Dalbergia nigra (Vell.) Allemao ex Benth., two Fabaceae endangered species from Brazilian Atlantic Forest. Analyses were performed in mature seeds (before) and after 1, 2, 5 and 8 days of imbibition for P. foliolosa and 2, 5, 8 and 11 days for D. nigra, corresponding to imbibition (phase I), root protrusion (phase II), root elongation and seedling (phase III) phases. Seeds of P. foliolosa complete germination before of D. nigra. The higher content of sucrose in the mature dry seed, and increasing contents of free spermidine and spermine during imbibition (phase I) and radicle protrusion (phase II) in P. foliolosa seeds could be related with the early germination in this species. The higher glucose contents and presence of maltose in mature dry seed and at the phases I and II might be associated with a more time necessary for seed germination in D. nigra. Free putrescine and fructose contents are necessary to seedling growth (phase III) in both species. This work is the first to report an association between these compounds during seed germination and early seedling growth in these species. This characterization can contribute to biochemical network of seed germination in wood species, and can be used in conservation programs of endangered species, as well as in biotechnological approaches to improve alternative methods of in vitro propagation, as somatic embryogenesis.