Abstract: The difference of melatonin concentration between day and night in leaves of Baikal skullcap (Scutellaria baicalensis) was examined by high-performance liquid chromatography with fluorescence detector, and melatonin content was detected and quantified in flowers and seeds too. The results show there is appreciable difference of melatonin concentration between the fresh leaves sampled in night and in day, 1.6503　ng/g and 0.5163 ng/g respectively. The melatonin concentration in flowers and seeds was also observed. The function of melatonin in plants is not completely clear now, but the research on the level of melatonin in plants will provide information helpful in nutrition, medicine and agriculture.