Since Myrtaceae is considered a complex family concerning the taxonomic classification due to the elevated number of components, difficult morphologic differentiation, and relatively low amount of studies in area, this article describes the potentiality of classification using chemometrics applied to UPLC-qToF/MS-MS dataset for chemotaxonomy investigation of leaves of fifteen species from the genus Psidium, Plinia, Myrciaria, and Eugenia into the Myrtaceae family. The use of a multivariate tool was indispensable to detect marker compounds since an elevated number of information on chromatograms did not provide conclusive data. The results offered an adequate classification among genus and species, principally based on ellagic acid, catechin, epicatechin, isoquercitrin, quercitrin, reynoutrin, madecassic acid, asiatic acid, and morin, used as marker compounds. Therefore, the method was useful and permitted the satisfactory chemotaxonomic distinction among the genus.