Abstract Problems with identification and labeling of medicinal plants, as well as substitution/adulteration of non-toxic plants by toxic ones have previously led to cancer, renal failure and even deaths. The non-toxic Stephania tetrandra (Fangji) has been known to be substituted by Aristolochia fangchi (Guang fangji), which contains the nephrotoxic and carcinogenic aristolochic acid (AA). In this study, 10 samples of “Fangji” were bought from local medicinal shops. HPLC-DAD chromatographic fingerprints of each methanol extract were compared with those of A. fangchi and S. tetrandra, using aristolochic acid I (AAI), tetrandrine and fangchinoline as marker compounds. Nine of the samples were found to be similar to A. fangchi. The presence of AAI in the nine samples was confirmed using LC-MS/MS. Neither tetrandrine nor fangchinoline were detected in these samples. The methods developed in this study allow the simultaneous detection of AAI, fangchinoline and tetrandrine. The results suggest possible substitution of S. tetrandra by A. fangchi at wholesale or retail level. This study highlights the importance of greater control of medicinal plants with toxic components as these may still be readily accessible to the public.