This study enhances the current limited understanding of the interaction between mercury (Hg) and selenium (Se) species in fish. Rainbow trout (Oncorhynchus mykiss), a model aquaculture fish, was exposed to Hg and Se species through controlled dietary conditions. Over a 6-month feeding trial, the impact of dietary Se on Hg bioaccumulation in fish, including flesh, brain, and liver, was tracked. Twelve dietary conditions were tested, including plant-based diets (0.25 µgSe g−1) and tuna byproduct diets (0.25 µgHg g−1, 8.0 µgSe g−1) enriched with methylmercury and/or Se as selenite or selenomethionine. The tuna byproduct diet resulted in lower Hg levels than the plant-based diets, with muscle Hg content below the European Commission's safe threshold. This study highlights the significant impact of specific Se compounds in the diet, particularly from tuna-based aquafeed, on Hg bioaccumulation. These promising results provide a strong recommendation for future use of fisheries byproducts in sustainable aquafeeds.