The selection of genetically superior materials of different forest species with economic potential involves studies of germplasm characterization. Facing the exploitation of aroeira (Schinus terebinthifolius Raddi.) in areas of natural occurrence the genetic and chemical characterization of individuals is extremely important to suit the selection. The work was carried out to identify genetic and chemical differences in individuals of aroeira located in different forest fragments. The genetic polymorphism was accessed using 19 inter-simple sequence repeat (ISSR) primers and the fragments generated were used to evaluate the Nei's gene diversity, percentage of polymorphic loci, Shannon index, number of alleles observed and effective number of alleles. The fruits of all individuals were submitted to hydro distillation of essential oils. The oil chemistry composition was analyzed by Gas chromatography/mass spectrometry (GC/ME) and the averages of the compounds were compared by Scott-Knott (p<0.05). The correlations using genetic, geographic distances and chemical composition were analyzed by the Mantel test. There are considerable levels of genetic and chemistry variability among the individuals studied, which allows markers assisted selection aiming to identify potential genitors for use in plant breeding. Key words: Aroeira, genetic polymorphism, inter-simple sequence repeat (ISSR), poivre-rouge, volatile chemicals.