The present work deals with the development and validation of a novel dual CD‐MEKC system for the systematic flavonoid fingerprinting of Ligaria cuneifolia (R. et P.) Tiegh.—Loranthaceae—extracts. The BGE consisted of 20 mM pH 8.3 borate buffer, 50 mM SDS, a dual CD system based on the combination of 5 mM β‐CD and 2% w/v S‐β‐CD, and 10% v/v methanol. The proposed method has been successfully applied to the comparative analysis of extracts from aerial parts and different hosts, geographical areas, and extraction procedures in order to establish the flavonoid fingerprint of L. cuneifolia. The method was validated according to international guidelines. LOD and LOQ, intra and interday precision, and linearity were determined for catechin, epicatechin, procyanidin B2, rutin, quercetin‐3‐O‐glucoside, quercetin‐3‐O‐xyloside, quercetin‐3‐O‐rhamnoside, quercetin‐3‐O‐arabinofuranoside, quercetin‐3‐O‐arabinopyranoside, and quercetin. The CD‐MEKC methodology emerges as a suitable alternative to the traditional HPLC for quality control, fingerprinting, and standardization of L. cuneifolia extracts from different sources.