Two native species in the San Francisco Estuary, California, that are in decline are the threatened longfin smelt (Spirinchus thaleichthys) and endangered delta smelt (Hypomesus transpacificus). Abundances have reached record lows and these populations are at imminent risk of extirpation. We exposed longfin smelt and delta smelt to environmentally-relevant temperatures (14°C, 20°C) and used RNA-sequencing to examine the transcriptome-wide responses to elevated water temperature in both species. Post-larval (~42 days post hatch) fish were acclimated to 14°C for eight days prior to the temperature treatments. One subset of fish was acutely exposed to 20°C and then allowed 60 min recovery at 14°C prior to sampling. The other group was handled the same way, however remained at 14°C. Total RNA (whole fish) from ten fish from each species (five from each temperature treatment) was used to prepare 20 libraries with unique adapters. Each species was sequenced on an Illumina HiSeq2500 over two lanes (two lanes per species). Two different species-specific reference transcriptomes were assembled and used for the differential expression analyses.