This research is part of an ongoing selection and breeding effort to target Iranian genotypes of Hypericum perforatum with the potential to produce higher amounts of desired secondary metabolites and greater resistance to fungal pathogens. There is a significant interest in the development of such cultivars to supply materials to the local pharmaceutical industries. For this reason, two improved cultivars of H. perforatum (“Gold” and “Veperikon”) were compared with a wild Iranian population (Ardabile population) under common garden conditions in Iran. Plants were cultivated from seed in a greenhouse and seedlings were transplanted after one month to the field plots. The statistical design of this study was a Randomized Complete Block Design with three replications. During the period of full flowering, selected phenological (number of days to flowering), morphological (plant height, mean leaf area, number of black glands/leaf) and chemical (hypericin and pseudohypericin content) characteristics were assessed. Our observations were that the “Veperikon” cultivar is very sensitive to soil-borne diseases. All transplanted seedlings were infected by the plant pathogenic fungus Colletotrichum gloeosporioides, which caused necrosis of the whole plant. Both the “Gold” cultivar and plants from the wild population persisted despite mild infections with C. gloeosporioides and produced flowering shoots at both the first and second years after cultivation. The “Gold” cultivar was superior to the Ardabile population in terms of phenological and morphological characteristics. The average naphthodianthrone content (% dry weight of tissue) for the wild Iranian population was 0.04(±0.01)%, but for the “Gold” cultivar, 0.33(±0.43)%. These data indicate that selection and directed cultivation of Iranian H. perforatum plants can result in plants with improved morphological, phenological and chemical characteristics.