The objective of present study was to establish and compare the contents of secondary metabolites of two Hypericum species, H. perforatum and H. maculatum, native to Lithuania, and to evaluate factors predetermining their variation with some practical implications for utilization and conservation. The HPLC analysis of the ethanolic extracts of the studied species showed some regularity in their composition. Both species contained chlorogenic acid, hyperoside, quercitrin, quercetin and hypericin. The presence of rutin and hyperforin was observed only in H. perforatum. The quantitative analysis showed higher content of quercitrin in H. perforatum, than in H. maculatum, whereas the differences in the contents of quercetin, hypericin and chlorogenic acid were not statistically significant between the species. H. maculatum contained a significantly higher content of hyperoside than H. perforatum. The data on phytochemical analysis suggest almost equivalent use of both H. perforatum and H. maculatum extracts in the food industry, cosmetics and pharmaceutics.