Cariniana estrellensis (Raddi) Kuntze seedlings have been used in forest restoration programs in the Atlantic Forest biome. However, despite the economic and ecological relevance of this species, to date no general method for rapid identification of primary and secondary metabolites of C. estrellensis leaves has been reported. In this work, we explore the feasibility of using rapid analysis by nuclear magnetic resonance techniques and liquid chromatography coupled to diode array, charged aerosol, and mass detection. The main secondary metabolites identified were hydrolysable tannins, quinic acid, hydroxycinnamic acids (trans-p-coumaric acid, cis-p-coumaric acid, and trans-ferulic acid), and flavonoids (kaempferol and quercetin derivatives). These compounds are particularly useful as chemotaxonomic markers for the genus Cariniana and for the family Lecythidaceae, and may also be important for pharmacological uses and for the survival of the seedlings in reforestation programs.