The advance of NGS technologies opened exciting research avenues, as for example expanding the study of the mechanisms underlying adaptation from model organisms to natural systems. We used NGS technologies to sequence 12 RNA-seq libraries, and provide the first transcriptomes of two endemic Iberian Cyprinids. The species Squalius carolitertii and S. torgalensis inhabit different regions of Portugal with distinct climate types, Atlantic in the North and Mediterranean in the South, respectively. While northern regions present mild temperatures, in southern regions fish are often under harsh temperatures and droughts. Herein, we sequenced the transcriptome from three tissues (skeletal muscle, liver and fins) in an Illumina HiSeq2000 of fish exposed to different temperatures: 18ºC (control) and 30ºC (test). Around 200 million raw reads were generated for each species, with similar number of reads per library (approximately 30 million), rendering de novo assemblies with a total of 145975 and 137303 contigs, for S. carolitertii and S. torgalensis, respectively. Gene ontology showed that around 60% of the annotated genes belonged to four biological processes and approximately 75% to two molecular functions. Besides, this study provides, for the first time, the transcriptome characterization of two endemic fish from Iberian freshwater basins, S. carolitertii and S. torgalensis, and constitutes a valuable resource for understanding environmental adaptations of Iberian Cyprinids.