Thermal variability significantly impacts fish performance, and current breeding objectives may soon be suboptimal due to climate change. Growth is a critical trait for aquaculture profitability. Understanding the genomic differences in growth under varying water temperatures is essential to predict climate change's impact on cold water species production. This study examined a rainbow trout population grown under low (~ 7 °C) and high (~ 22 °C) non-lethal temperatures. The objectives were to: (i) explore the genetic architecture of growth under upper and lower temperature (UT and LT) conditions using multi-trait genome-wide association, and (ii) identify candidate genes and biological processes related to growth in these conditions through a gene-based meta-analysis approach. The results revealed: (i) significant genetic variation for body weight, body length, and average daily gain at both LT and UT conditions, with genomic heritabilities ranging from 0.19 ± 0.06 to 0.32 ± 0.05 and 0.16 ± 0.05 to 0.39 ± 0.08, respectively; (ii) distinct genetic architectures and genes associated with UT and LT growth, with SNP effect correlations from r = 0.06 to 0.22; (iii) shared biological functions for growth at UT and LT, involving cardiovascular function maintenance and cell communication. Cytoskeleton-related functions were predominant in growth at LT, while DNA repair functions were more significant at UT. Notably, sema6ba emerges as a potential candidate gene involved in growth-related traits across contrasting thermal environments in rainbow trout, given its strong association under both low and high temperature conditions.