Abstract: Two simple and efficient methods have been developed for screening and identification of natural peroxynitrite scavengers in Radix Scrophulariae (RS). Method I was based on HPLC-DAD-(luminol-peroxynitrite)-CL techniques combined with Q-TOF MS/MS analysis, while method II was based on the pre-column reaction with peroxynitrite followed by HPLC separation with Q-TOF MS/MS analysis. Five active constituents, P1(decaffeoylacteoside), P9(eoside), I6(6″-O-feruloylharpagide), P11(cis-acteoside)and P13(angoroside), were found to possess potential peroxynitrite-scavenging activity by method I, while P9 and P13 were also screened by method II. Method I requires more complex apparatus, but has advantages on simple detection and high sensitivity. Method II requires simpler apparatus than method I, but with more tedious detection and lower sensitivity. However, the methods established above would provide new ways for rapid detection of natural peroxynitrite-scavenging compounds in RX complex matrices.