The genus Aquilaria Lam. (Thymelaea-ceae) comprises 21 tree species (The Plant List, 2013) and is mostly found in Southeast Asia. When the tree is infected (fungi, bacteria), its wood turns brownish or blackish (then called agarwood) due to the secretion of an oleoresin as a reaction to the infection. The resin is very fragrant and has been sought after and used for centuries by Buddhists, Hindus and Muslims to make incense for religious ceremonies. This oleoresin is mainly found in species of the genus Aquilaria, but also in a few species of the genera Gyrinops Gaertner and Gonystylus Teijsmann & Binnendijk. It is difficult to distinguish between these species, and this lack of taxonomic knowledge has led to over-use of the trees and endan-gering these endemic species listed in CITES Appendix II. We used chemotaxo-nomy as a discrimination tool to ana-lyse polyphenolic molecules, which are secondary metabolites and known to act as taxonomic markers in other plants. Using a simple, effective and inexpen-sive analysis technique (two-dimensional thin-layer chromatography), we found the same polyphenolic molecule in the six species of the genus Aquilaria we stu-died, which was identified as mangife-rin by chromatographic and colorimetric analysis in comparison with a mangiferin control molecule. During these analyses, we found a relationship between the genera Aquilaria and Gyrinops (botani-cally demonstrated) in the occasional existence of mangiferin in three species of the genus Gyrinops. We also found that a time laps of 140 years between two herbarium samples of the same species had virtually no effect on the mangiferin concentration in the plant. This study showed the merits of chemotaxonomy in seeking taxonomic markers, and the ori-ginality of colorimetric analysis of a thin-layer chromatographed plant metabolite.