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[Display omitted] • Hg concentration in fish was below the maximum residual limit (MRL) • Hg levels in fish found in the following order: pelagic > benthic > demersal. • Both Se and Hg levels biomagnified in the food web along the Gulf of Mannar coast. • Se: Hg molar ratio was > 1, suggesting a protective effect of Se on Hg toxicity. • Health risk analysis (THQ/HI < 1) indicates fish collected from this region was safe. • Se-HBV and HBVse showed fishes were the surplus source of Se and mitigating Hg toxicity. This study aimed to explore the concentrations of Se and Hg in marine fish along the Gulf of Mannar (southeast coast of India) and to assess related risks and risk-based consumption limits for children, pregnant women, and adults. Se concentrations in pelagic and benthic fish ranged from 0.278 to 0.470 mg/kg and 0.203 to 0.294 mg/kg, respectively, whereas Hg concentrations ranged from 0.028 to 0.106 mg/kg and 0.026 to 0.097 mg/kg, respectively. Se and Hg contents in demersal fish (Nemipterus japonicus) were 0.282 and 0.039 mg/kg, respectively. The lowest and highest Hg concentrations in pelagic fish were found in Scomberomorus commersoni and Euthynnus affinis whereas the lowest and highest Se concentrations in benthic fish were found in Scarus ghobban and Siganus javus. Se concentrations in marine fishes were found in the following order: pelagic > demersal > benthic whereas Hg concentrations were found in the following order: pelagic > benthic > demersal. The presence of Se in fish was positively correlated with trophic level (TL) and size whereas that of Hg was weakly correlated with TL and habitat and negatively correlated with size. Se risk–benefit analysis, the AI/RDI (actual intake/recommended daily intake) ratio was > 100 % and the AI/UL (upper limit) ratio was < 100 %, indicating that all fish have sufficient levels of Se to meet daily requirements without exceeding the UL. Hg level was below the maximum residual limit (MRL) of 0.5 mg/kg for most fish but it was 1 mg/kg in E. affinis and Lethrinus lentjan. The target hazard quotient (THQ < 1) and hazard index (HI < 1) imply that the consumption of fish poses no noncarcinogenic health risks. However, all examined fish had a mean Se/Hg molar ratio > 1, indicating that human intake of fish was rather safe relative to Hg content. Health benefit indexes (Se-HBV and HBVse) with high positive values in all fish supported the protective effect of Se against Hg toxicity, suggesting the overall safety of fish consumption. The high Se/Hg ratio in fish could be attributed to the replacement of Se bound to Hg, thereby suppressing Hg toxicity and maintaining normal selenoprotein synthesis. This insight is useful for a better understanding of food safety analysis. [ABSTRACT FROM AUTHOR]