The increasing use of alternative feeds for sustainable aquaculture leads to a reduced selenium content requiring the use of supplements to maintain the antioxidant status of farmed fish. The introduction of tuna by-products in fish feed is attractive for their selenium content, but the presence of mercury limits their use as it may negatively impact fish health. Indeed, selenium and mercury metabolism, in relation to their interaction and biological effects in fish, is far from being fully understood. This study aims to assess the impact of parental and dietary supplementation with selenomethionine and methylmercury on selenium and mercury localisation and concentrations in tissues of 3-week rainbow trout fry. Six diets were used. Broodstock were fed a plant-based diet Bpc (with 0.2 μg g−1 selenium and 0 μg g−1 mercury) or a tuna by-product-based diet Bt (with 4 μg g−1 selenium and basal mercury at 0.2 μg g−1) during 6 months, supplemented or not with 4 μg g−1 of selenomethionine for the plant-based diet Bpo and/or with 2 μg g−1 of methylmercury for diets Bph, Bpho and Bth. Their offspring were fed the plant-based diet Fpc, supplemented or not with the same levels of selenomethionine and methylmercury, until their third week. Mercury and selenium concentrations were determined in fry whole-body by ICP MS and quantitative images of selenium and mercury were produced by LA–ICP MS from fry whole-body thin sections. Dietary supplementation of fry with selenium and/or mercury increased their concentration in all tissues, especially in liver, kidney, muscle and intestine. Parental selenomethionine supplementation had a more pronounced effect on fry selenium levels than tuna by-products diet. Mercury transfer from broodstock to their offspring was weak. Mercury concentrations decreased in the kidney of fry supplemented with both selenium and mercury, which could be related to the presence of selenium.