Flavonoid composition and concentration were investigated in 12 different tissues of ‘Ti-1’ lotus (Nelumbonucifera) by high performance liquid chromatography equipped with photodiode array detection tandem electrospray ionization mass spectrometry (HPLC-DAD-ESI-MSn). A total of 20 flavonoids belonging to six groups (myricetin, quercetin, kaempferol, isohamnetin, diosmetin derivatives) were separated and identified. Myricetin 3-O-galactoside, myricetin 3-O-glucuronide, isorhamnetin 3-O-glucuronide and free aglycone diometin (3_,5,7-trihydroxy-4_-methoxyflavone) were first reported in lotus. Flavonoid composition varied largely with tissue type, and diverse compounds (5–15) were found in leaf and flower stalks, flower pistils, seed coats and embryos. Flower tissues including flower petals, stamens, pistils, and, especially, reproductive tissue fruit coats had more flavonoid compounds (15–17) than leaves (12), while no flavonoids were detectable in seed kernels. The flavonoid content of seed embryos was high, 730.95 mg 100 g？1 DW (dry weight). As regards the other tissues, mature leaf pulp (771.79 mg 100 g？1 FW (fresh weight)) and young leaves (650.67 mg 100 g？1 FW) had higher total flavonoid amount than flower stamens(359.45 mg 100 g？1 FW) and flower petals (342.97 mg 100 g？1 FW), while leaf stalks, flower stalks and seed coats had much less total flavonoid (less than 40 mg 100 g？1 FW).