Background and Aims Hypericum perforatum is a perennial herbaceous plant and an extract from this plant has a significant antidepressant effect when administered to humans. The plant is characterized by its secretory glands, also known as dark glands, which are mainly visible on leaves and flowers. The current study evaluates the influence of several environmental factors and developmental stages of the plant on the accumulation and synthesis of hypericin and pseudohypericin (Hy-G), the major bioactive constituents, in H. perforatum plants.Methods The appearance of dark glands on different parts of the plant, under several environmental conditions, was monitored by microscopy. Hy-G concentrations were quantified by high-performance liquid chromatography.Key Results A significant presence of dark glands accompanying the highest concentrations of Hy-G was observed in the stamen tissues more than in any other organ of H. perforatum. A linear relationship between the number of dark glands and net photosynthetic rate of the leaf and Hy-G concentration in the leaf tissue was also established. A very high concentration of Hy-G was measured in the dark-gland tissues, but in the tissues without any dark glands it was almost absent. The presence of emodin, a precursor of Hy-G, at a high concentration in the dark-gland tissues, and its absence in the surrounding tissues was also observed, suggesting that the site of biosynthesis of Hy-G is in the dark-gland cells. A significantly low concentration of Hy-G (occasionally non-detectable) was measured in the xylem sap of the stem tissues. The dark-gland tissues collected from leaves, stems or flowers contained similar concentrations of Hy-G.Conclusions The concentration of Hy-G in various organs of H. perforatum plants is dependent on the number of dark glands, their size or area, not on the location of the dark glands on the plant. The study provides the first experimental evidence that Hy-G is synthesized and accumulates in dark glands.