High‐performance liquid chromatographic (HPLC) and flow‐injection mass spectrometric (FIMS) fingerprinting profiles were used to differentiate between wild and artificial cultivated Stephaniae tetrandrae Radix samples. HPLC and FIMS fingerprints of 15 wild S. tetrandrae Radix samples and 12 artificial cultivated S. tetrandrae Radix samples were obtained and analyzed with the aid of principal component analysis (PCA). PCA of the fingerprints showed that the chemical differences between wild and artificial cultivated S. tetrandrae Radix samples could be differentiated by either HPLC or FIMS fingerprints. The HPLC fingerprints provided more chemical information but required longer analytical time compared with FIMS fingerprints. This study indicated that the wild samples contained higher concentrations of almost all of the major compounds than the cultivated samples. Three characteristic compounds which were responsible for the differences between the samples were tentatively identified with the aid of MS data. Furthermore, these three compounds, tetrandrine (TET), fangchinoline (FAN), and cyclanoline (CYC), were quantified. The HPLC and FIMS fingerprints combined with PCA could be used for quality assessment of wild and artificial cultivated S. tetrandrae Radix samples.