The present study was conducted to determine phenologic and morphogenetic variation of hypericin, chlorogenic acid and flavonoids, as rutin, hyperoside, apigenin-7-O-glucoside, quercltrin, quercetin content of Hypericum perforatum L. growing in Turkey. Wild growing plants were harvested at vegetative, floral budding, full flowering,fresh fruiting and mature fruiting stages and dissected into stem, leaf and reproductive tissues and assayed for bioactive compounds by the High performance liquid chromatography (HPLC) method. Hyperlcin concentration ranged between 0 and 2.73 mg/g DW, chlorogenic acid 0.00-3.64 mg/g DW, rutin 0.00-3.36 mg/g DW, hyperoside 0.04-22.42 mg/g DW, quercitrin 0.03-3.45 mg/g DW and quercetin 0.04-1.02 mg/g DW depending on ontogenetic and morphogenetic sampling. Leaves were found to be superior to stems and reproductive parts with regard to phenolic accumulation for all compounds tested while flowers accumulated the highest levels of hypericin. Quercitrin,quercetin and hypericin content in all tissues increased with advancing of developmental stages and reached their highest level during flower ontogenesis. Similarly, chlorogenic acid, hyperoside and apigenin-7-O-glucoside content in different plant parts increased during plant development, however, the highest level was observed at different stages of plant phenology for each tissue. Chlorogenic acid was not detected in stems, leaves and reproductive parts in several stages of plant phenology and its variation during plant growth showed inconsistent manner. In contrast to the other compounds examined, rutin content of stems and leaves decreased with advancing of plant development and the highest level for both tissues was observed at the vegetative stage. However,content of the same compound in reproductive parts was the highest at mature fruiting. The present findings might be useful to obtain increased concentration of these natural compounds.