The flowers constitute one of the main sites of accumulation of phenolic compounds in plants of the Hypericum genus. In addition to their important pharmacological activities, some metabolites found in species from the section Brathys and Trigynobrathys appear to have chemotaxonomic significance according to the literature. HPLC analyses were carried out to assess the pattern and accumulation of the dimeric phloroglucinols, benzophenones, benzopyrans, flavonoids and a phenolic acid in flowers of Hypericum species native to southern Brazil and Peruvian Páramos. Qualitative and quantitative differences are reported. Uliginosin B and hyperoside were the main components detected in all species and with maximum concentrations up to 0.188% in H. caprifoliatum and 5.987% in H. andinum, respectively. The content of japonicin A varied from 0.003 to 0.087% in H. myrianthum, while the yield of hyperbrasilol B ranged from 0.006% in H. laricifolium to 0.011% in H. caprifoliatum. The major compounds in H. polyanthemum and H. carinatum were the benzopyrans 6-isobutyryl-5,7-dimethoxy-2,2-dimethylbenzopyran (HP1 = 0.200%), 7-hydroxy-6-isobutyryl-5- methoxy-2,2-dimethyl-benzopyran (HP2 = 0.225%) and 5-hydroxy-6-isobutyryl-7-methoxy-2,2-dimethyl-benzopyran (HP3 = 0.327%) and benzophenones cariphenone A (0.309%) and cariphenone B (0.062%), respectively. Maximum amounts of chlorogenic acid, isoquercitrin, quercitrin and guaijaverin were observed, respectively, in H. campestre (1.458%), H. andinum (1.161%), H. carinatum (0.231%) and H. laricifolium (0.404%). The results obtained support the taxonomic evidence of the dimeric phloroglucinol derivatives at the section level.