An efficient and accurate fingerprinting method using reversed-phase rapid-resolution liquid-chromatography coupled with photodiode array detection has been developed and optimized to examine the variance in active compounds among Ziziphora clinopodioides Lam from different locations. Three active components, diosmin, linarin and pulegone, were identified by matching their retention times and UV spectra with the corresponding reference compounds. Our results indicated that chromatographic fingerprints, in combination with principal component analysis (PCA) and hierarchical clustering analysis (HCA), could efficiently identify and distinguish Z. clinopodioides from different sources. Our fingerprinting methods and data will be useful for quality control, and thus, more effective dosing in clinical application of Z. clinopodioides.