Selenium (Se) deficiency is a problem widely encountered in humans and terrestrial livestock production with increasing attention also in aquaculture. Se supports the antioxidant system, which becomes especially important during stressful conditions. In the present study, the effect of Se-supplementation in broodstock and fry diets on the performance and antioxidant metabolism of rainbow trout fry under acute hypoxia was investigated. Rainbow trout broodstock were fed plant-ingredient based diets either without any Se-supplementation (Se level: 0.3 mg/kg) or supplemented with Se supplied as sodium selenite or as hydroxy-selenomethionine (Se level: 0.6 mg/kg respectively) for 6 months prior to spawning. The progenies were subdivided into three triplicate feeding groups and fed diets with similar Se levels compared to the parental diets, resulting in a 3x3 factorial design. After 11 weeks of feeding, the fry were either sampled or subjected to a hypoxic stress challenge. One hundred fish were transferred to tanks containing water with a low oxygen level (1.7 ± 0.2 ppm) and monitored closely for 30 min. When a fish started to faint it was recorded and transferred back to normoxic water. Direct fry feeding of the hydroxy-selenomethionine supplemented diet improved the resistance towards the hypoxic stress. On the contrary, fry originating from parents fed Se-supplemented diets showed a lower stress resistance compared to fry originating from parents fed the control diet. Fry subjected to hypoxia showed elevated oxidative stress with reduced glutathione (GSH) levels and increased isoprostanes (IsoP) and phytoprostanes (PhytoP) levels produced by lipid peroxidation of polyunsaturated fatty acids (PUFA), arachidonic and αlinolenic acids respectively. Increased mRNA expression of transcription factors (nrf2, nfκb, keap1X2) and decreased mRNA expression of antioxidant enzymes (trxr, sod, gstπ) indicated a transcriptional regulation of the antioxidant response. In stressed fry, the mRNA expression of several antioxidant genes including gr, msr and gstπ was found to be higher when fed the control diet compared to the sodium selenite treatment, with a contrary effect for parental and direct Se nutrition on gpx. The long-term parental effect becomes of greater importance in stressed fry, where more than half of the genes were significantly higher expressed in the control compared to the selenite supplemented group.