Herba Epimedii (family Berberidaceae), Yinyanghuo in Chinese, is one of commonly used Chinese medicines. Flavonoids are considered as its active components. In this study, a simple and reliable capillary zone electrophoresis (CZE) method was developed for simultaneous determination of sixteen flavonoids ,namely epimedin B, epimedin A, hexandraside F, epimedin C, icariin,sagittatoside B, sagittatoside A, hexandraside E, 2"-O-rhamnosyl icariside II, baohuoside VII, baohuoside l, caohuoside C, epimedoside C, baohuoside II, hyperoside and kaempferol-3-O-rhamnoside in different species of Epimedium using rutin as internal standard (IS). The analysis was performed within 30 min by using 50 mM borate buffer (pH10.0) containing 20% acetonitrile as modifier, while separation voltage was 25 kV and temperature was at 30℃. All calibration curves showed good linearity (r2>0.9948)within test ranges. The LOD and LOQ were lower than 7.8 μg/mL and 38.8 μg/mL, respectively. The overall RSDs for intra- and inter-day of sixteen analytes were less than 4.7%, and the recoveries were 97.1%-106.2%. Different species of Epimedium samples were analyzed using the validated method, which is useful to control the quality of Epimedium and its medical preparations.