Massive macroalgae blooms, primarily caused by the overgrowth of Ulva prolifera (U. prolifera) in the Yellow Sea of China, pose a severe risk to both marine organisms and the aquaculture industry. This study’s aim was to evaluate the impact of U. prolifera degradation on the growth performance and antioxidant capacity of Japanese flounder (Paralichthys olivaceus) and select some potential Japanese flounder families (labeled 2101–2108, established by crossbreeding) tolerating U. prolifera degradation conditions. Thus, a 60-day U. prolifera exposure experiment was conducted. The results showed that the contents of Na, K, Mg, and Fe elements in the U. prolifera degradation water were significantly increased. The specific growth rate and survival rate of flounder were significantly decreased under the U. prolifera degradation condition, while the 2101 and 2103 flounder families showed a better growth performance compared with the positive control (PC) group. Moreover, the results showed that activities of total antioxidant capacity (T-AOC), transaminases, and alkaline phosphatase (AKP) in serum were significantly decreased, while the 2103 flounder family showed higher activities. Furthermore, U. prolifera degradation significantly increased superoxide dismutase (SOD) activity and glutathione (GSH) content while decreasing catalase (CAT) activity and malondialdehyde (MDA) content in the liver. Specifically, SOD and CAT activities of the 2103 flounder family were higher than the 2101 flounder family and PC group. In addition, the gill SOD and CAT activities of the 2103 flounder family were significantly higher than the PC group. Similarly, the antioxidant-related gene (sod and cat) expressions were synchronously upregulated or downregulated in the liver and gills in response to U. prolifera degradation. These results revealed that U. prolifera degradation decreased the growth performance and influenced the antioxidant capacity of Japanese flounder, while the 2103 flounder family had better advantages in the U. prolifera degradation condition. Therefore, the 2103 flounder family could be regarded as the potential flounder family tolerating U. prolifera degradation. The increased Fe content in the U. prolifera degradation water may be one of the main causes of the physiological alterations observed in Japanese flounder.
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