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Despite their relatively poorly investigated phytochemistry, species of the genus Chuquiragaare widely commercialized. The present study reports the use of a high-resolution liquid chromatography–mass spectrometry-based metabolomics approach coupled with exploratory and supervised multivariate statistical analyses for species classification and chemical marker identification of four species of Chuquiraga(C. jussieui, C. weberbaueri, C. spinosa, and Chuquiragasp.) from Ecuador and Peru. Based on these analyses, a high percentage of correct classifications (87% to 100%) allowed the prediction of the taxonomic identity of Chuquiragaspecies. Through the metabolite selection process, several key constituents with the potential to be chemical markers were identified. Samples of C. jussieuidisplayed alkyl glycosides and triterpenoid glycosides as discriminating metabolites, while Chuquiragasp. displayed high concentrations of p-hydroxyacetophenone, p-hydroxyacetophenone 4-O-glucoside, p-hydroxyacetophenone 4-O-(6-O-apiosyl)-glucoside, and quinic acid ester derivatives as the main metabolites. Caffeic acid was characteristic for C. weberbauerisamples, whereas C. spinosadisplayed higher concentrations of the following new phenylpropanoid ester derivatives: 2-O-caffeoyl-4-hydroxypentanedioic acid (24), 2-O-p-coumaroyl-4-hydroxypentanedioic acid (34), 2-O-feruloyl-4-hydroxypentanedioic acid (46), 2,4-O-dicaffeoylpentanedioic acid (71), and 2-O-caffeoyl-4-O-feruloylpentanedioic acid (77).