One feature of the Protium genus is the presence of secretory ducts associated with the phloem. These ducts are characterized by the production of essential oils with different classes of secondary metabolites. In light of this observation, the purpose of this study was to determine which secondary metabolites are present in the secretory ducts of P. aracouchini, P. heptaphyllum, P. icicariba and P. warmingianum using histochemical tests and essential oil chemical analysis. The essential oils are present at different levels and compositions in the four studied species; other metabolites also varied from species to species. Variation was observed among the essential oil classes with oxygenated sesquiterpenes being the most representative class found in the species studied. The major component of all species was caryophyllene oxide; thus, it may be regarded as a genus characteristic. Through the results obtained, characteristics common to all species were defined, enabling the segregation of the species and the use of these commonalities in taxonomic studies of the genus.