► First report five flavonoids in lotus leaves. ► An optimization on the extraction of lotus leaves is made. ► The method has been well validated. ► Composition and content of flavonoids in lotus largely depend on genetic background. The extraction protocol of flavonoids from lotus (Nelumbo nucifera) leaves was optimized through an orthogonal design. The solvent was the most important factor comparing solvent, solvent:tissue ratio, extraction time, and temperature. The highest yield of flavonoids was achieved with 70% methanol–water and a solvent:tissue ratio of 30:1 at 4°C for 36h. The optimized analytical method for HPLC was a multi-step gradient elution using 0.5% formic acid (A) and CH3CN containing 0.1% formic acid (B), at a flow rate of 0.6mL/min. Using this optimized method, thirteen flavonoids were simultaneously separated and identified by high performance liquid chromatography coupled with photodiode array detection/electrospray ionization mass spectrometry (HPLC/DAD/ESI-MSn). Five of the bioactive compounds are reported in lotus leaves for the first time. The flavonoid content of the leaves of three representative cultivars was assessed under the optimized extraction and HPLC analytical conditions, and the seed-producing cultivar ‘Baijianlian’ had the highest flavonoid content compared with rhizome-producing ‘Zhimahuoulian’ and wild floral cultivar ‘Honglian’.