Bioamines play important roles in organisms, including controlling the biosynthesis of nucleic acids and stabilizing their structure to prevent denaturation. However, excessive intake of bioamines within a short period can inhibit the detoxification system. Meanwhile, excessive bioamines can damage the human body, even proving fatal. Pelagic marine fish such as Scomber japonicus and Engraulis japonicus are rich in ornithine, histidine and other amino acids, and related proteins. However, these compounds are easily decomposed by endogenous and exogenous enzymes during the storage of fish, resulting in the rapid production of several biogenic amines. Hence, they are labelled as fish with high biogenic amines. Several pelagic marine fish resources—an indispensable and important fishery resource in China and even globally—are at risk of high biogenic amine content. Here, we aimed to investigate the variations in different indicators during the spoilage of high biogenic amine fish and identify appropriate storage methods for them. S. japonicus and E. japonicus, two important pelagic fishes and typical high biogenic amine fishes in the eastern coastal areas of China, were selected as research subjects. Different indicators were assessed during the spoilage process, including pH, biogenic amine content, and volatile gas. Logistic analysis of biogenic amine content and linear discriminant analysis of volatile gas were performed. We found that S. japonicus and E. japonicus should not be stored for more than 3 days in cold temperatures (4 ℃). When S. japonicus was stored for ＞ 18 h and E. japonicus for ＞ 12 h at room temperature (25 ℃), significant changes were observed in their flavor and safety. Freezing temperature is the suitable storage temperature for S.japonicus and E. japonicus. Generally, the content of histamine in fish with high biogenic amine is higher than that of other biogenic amines; however, our study revealed that the content and change rate of cadaverine are higher than that of histamine in E. japonicus during the spoilage process. Therefore, cadaverine may be used as an indicator of the spoilage stage of E. japonicus, and detecting cadaverine in certain fish might better reflect the extent of spoilage compared to solely measuring histamine content. The results of this study provide theoretical support for the evaluating quality changes and safety control of fish with high biogenic amine. Moreover, they play a crucial role in early warning aimed at preventing poisoning associated with high biogenic amine fish.