A method based on high-performance liquid chromatography (HPLC) with diode array detector coupled with electrospray ionisation-mass spectrometry and an online detection system for radical scavenging was established and used to rapidly find and quantify antioxidant compounds in the water extracts of Hippocampus japonicus Kaup, Hippocampus kuda Bleeker and Syngnathus acus Linnaeus. The online screening results revealed the presence of one major radical scavenging compound identified as hypoxanthine by comparison of mass data and retention time with the standard. Subsequently, the developed HPLC method was applied to quantify hypoxanthine in different H. japonicus, H. kuda and S. acus samples. The results indicated that the developed HPLC method is simple and reliable for the quantification of hypoxanthine with a detection limit at 0.002 µg mL(-1), and a high recovery from 96.3% to 102.1%. This method provides a powerful tool for rapid identification and quantification of free radical scavenging compounds in complex marine natural products.