This study evaluated how different forms of Se supplementation into rainbow trout broodstock diets modified the one-carbon metabolism of the progeny after the beginning of exogenous feeding and followed by hypoxia challenge. The progeny of three groups of rainbow trout broodstock fed either a control diet (Se level: 0.3 μg/g) or a diet supplemented with inorganic sodium selenite (Se level: 0.6 μg/g) or organic hydroxy-selenomethionine (Se level: 0.6 μg/g) were cross-fed with diets of similar Se composition for 11 weeks. Offspring were sampled either before or after being subjected to an acute hypoxic stress (1.7 mg/L dissolved oxygen) for 30 minutes. In normoxic fry, parental Se supplementation allowed higher glutathione levels compared to fry originating from parents fed the control diet. Parental hydroxy-selenomethionine treatment also increased cysteine and cysteinyl-glycine concentrations in fry. Dietary Se supplementation decreased cgl mRNA levels. Hydroxy-selenomethionine feeding also lowered the levels of some essential free amino acids in muscle tissue. Supplementation of organic Se to parents and fry reduced bhmt expression in fry. The hypoxic stress decreased whole-body homocysteine, cysteine, cysteinyl-glycine and glutathione levels. Together with the higher mRNA levels of cbs, a transsulfuration enzyme, this suggests that under hypoxia, glutathione synthesis through transsulfuration might have been impaired by the depletion of a glutathione precursor. In stressed fry, S-adenosylmethionine levels were significantly decreased, but S-adenosylhomocysteine remained stable. Decreased bhmt and amd1a mRNA levels in stressed fry suggest a nutritional programming by parental Se also on methionine metabolism of rainbow trout