Epimedium herb (Yinyanghuo), one of the popular Chinese materia medica, is a multiple species colony of Epimedium genus belonging to Berberidaceae. There are five species of Epimedium that have been officially adopted in Chinese Pharmacopoeia under the same crude drug name ‘Yinyanghuo’ comprising Epimedium brevicornu, E. koreanum, E. sagittatum, E. pubescens, and E. wushanense. In addition, non-official species like E. acuminatum, E. miryanthum and E. leptorrhizum are also mix-used. Frequently, the morphological taxonomical identification is very difficult during on-site inspection for species authentication in the market. Researchers are often bewildered by the multiple species ambiguity when putting this crude drug in use. Referring to the bioactive constituents that are vital for therapeutic efficacy, the key to clarifying the multiple species confusion should rely on analysis of the bioactive composition. It is well known that medicinal Epimedium herbs contain special C-8 prenylated flavonol glycosides which contribute to various bioactivities and the major four, epimedin A (A), epimedin B (B), epimedin C (C) and icariin (I), are unanimously used as bioactive markers for quality control. In this study, HPLC-DAD fingerprinting was performed for investigating the molecular spectrum of various Epimedium species. It was found that the four major flavonoids constitute the middle part of the chromatographic profiles to form a specific region (named as ‘ABCI fingerprint region’) being dominant in the HPLC profiles of all medicinal Epimedium species, and the five official species express five different ‘ABCI’ patterns (different peak: peak ratios). Our study found that the convergent tendency of the ‘ABCI region’ among multiple species of Epimedium could facilitate differentiation of complex commercial samples based on similar bioactive composition should confer similar bioactivities. Merging the different species that possess the same ‘ABCI region’ pattern into the same group can create a simpler bioactive-fraction-aided classification array by clustering the commercial samples into three bioactive ingredients-based fingerprint patterns – ‘E.b. pattern’, ‘E.k. pattern’ and ‘extensive E.w. pattern’. This approach offers the feasibility of characterizing and quality-controlling complex samples in the same genus designated under a single herbal drug entity on the premise of possessing the same bioactive ingredients pattern and supported by long-term traditional usage.