Data from: "Transcriptome resources for two non-model freshwater crustacean species" in Genomic Resources Notes accepted 1 October 2014 to 30 November 2014

The aim of this study was to characterize the whole transcriptomes of two common Mediterranean freshwater crustaceans: the copepod Eucyclops serrulatus (Fischer, 1851) and the amphipod Echinogammarus veneris Heller, 1865. Whole transcriptomic approaches may assist in studying the response to environmental pollution of species with little or no available genomic information, allowing the identification of genes involved in adaptation processes to polluted environments that can be studied in expression profile variation at a later stage. Further studies based on our results may allow for a more comprehensive overview of how freshwater crustaceans react to specific stressors, both from surface and groundwater habitats, where sub-lethal concentrations of individual stressors may become harmful when combined.