Total RNA from the skeletal muscle of each fish was obtained and sequenced using HiSeq Illumina technology. A total of 383,796,290 reads were mapped onto the reference Rainbow trout genome. RNA-seq analysis revealed that 293 genes were up-regulated in high-temperature group, mainly associated to autophagosome assembly, amino acid transport, and glutamine metabolic process. In the other hand, 119 genes were down-regulated in high-temperature group, mainly associated to digestion, proteolysis, and muscle contraction process. In addition, an increased LC3-II/LC3-I ratio measured by western blot analysis confirm skeletal muscle autophagy. This study offers an integrative analysis of the skeletal muscle response to high-temperature stress and reveals unknown aspects of this biological process in teleost