Transcriptional analysis is an important means for investigating the physiological response to environmental changes of nonmodel organisms, for which few genomic tools have been developed (Gracey 2007; Logan and Somero 2011; Garcia et al. 2012). Information from such studies can be particularly valuable in the conservation of threatened and endangered species, as in the case of the delta smelt, Hypomesus transpacificus (Connon et al. 2011a, b). Microarrays have been the predominant means of studying gene expression changes in salmonids following thermal stress (Arctic charr, Salvelinus alpinus) (Quinn et al. 2011), sockeye salmon, Oncorhynchus nerka (Jeffries et al. 2012; Jeffries et al. 2014), pink salmon, Oncorhynchus gorbuscha (Jeffries et al. 2014), rainbow trout, Oncorhynchus mykiss (Rebl et al. 2013), brown trout, Salmo trutta (Meier et al. 2014); to our knowledge, no other studies have examined the transcriptome-wide response of juvenile Chinook salmon to elevated temperatures. Here, we take an RNAseq approach to investigate gene expression changes associated with increased temperatures in juvenile Chinook salmon. This method offers a variety of improvements over microarrays for quantifying transcription. RNAseq allows for the examination of a large number of genes without necessitating prior knowledge of the gene sequences and it increases the accuracy of detection over a wide range of expression levels (Shendure 2008; Wang et al. 2009). Gill tissue was chosen for this experiment due to the complex physiological role of this organ and its rapid response to environmental stressors (Evans et al. 2005; Chou et al. 2008). The feasibility of nonlethal sampling of gill tissue also makes this a useful organ for future field studies (McCormick 1993; Schrock et al. 1994). By examining the suite of genes that are differentially expressed following thermal stress, we can identify groups of genes and cellular processes that may be important for responding to thermal stress in this species. This information may help us to identify thermal stress in wild fish through the use of gene expression assays, as well as provide candidate genes for the investigation of adaptation to thermal stress in future studies (see examples in Larsen et al. 2010; Wellband and Heath 2013).