Introduction Peroxynitrite is involved in the pathogenesis of a number of significant diseases. Peroxynitrite scavengers thus have potential application in understanding and treating these diseases. It is, therefore, important to establish screening methods able to rapidly identify peroxynitrite scavengers from herbal plants. Objective To develop effective and easily operable screening methods for identifying peroxynitrite scavengers in complex matrices, including Chinese herbal medicines. Methods Two simple and efficient screening methods have been developed for the identification of natural peroxynitrite scavengers in Flos Lonicerae Japonicae (FLJ). Method I used HPLC-DAD-(luminol-peroxynitrite)-CL techniques combined with Q-TOF MS/MS analysis, while Method II used pre-column reaction of the sample with peroxynitrite, followed by HPLC separation and Q-TOF MS/MS analysis. Results Five peroxynitrite scavengers (neochlorogenic acid, chlorogenic acid, 3,4-O-dicaffeoyl quinic acid, 3,5-O-dicaffeoyl quinic acid and 4,5-O-dicaffeoyl quinic acid) were identified in FLJ using Method I. Besides the compounds identified using Method I, three additional peroxynitrite scavengers (rutin, isoquercitrin and luteoloside) were identified using Method II. Conclusion The two new methods proved to be complementary and the use of these methods should allow rapid detection of peroxynitrite-scavenging natural products from FLJ and other complex matrices.