The emergence of pathogens represents substantial threats to public health, livestock, domesticated animals, and biodiversity. How wild populations respond to emerging pathogens has generated a lot of interest in the last two decades. With the recent advent of high-throughput sequencing technologies it is now possible to develop large transcriptomic resources for non-model organisms, hence allowing new research avenues on the immune responses of hosts from a large taxonomic spectra. We here focused on a wild population of the rostrum dace (Leuciscus burgiladensis) that is infected by Tracheliastes polycolpus, an emerging freshwater ectoparasite copepod. We used next generation Illumina sequencing technology to sequence the transcriptome of eight L. burdigalensis adult individuals collected in natura from the same sampling site. Four individuals were non-infected and four individuals were infected by T. polycolpus. We specifically focused on the spleen, the head kidney and epithelial cells and mucus from the fins, three tissues known to be involved in the immune response of fish. We used the Trinity methodology to reconstruct a de novo full-length transcriptome for L. burdigalensis. The resulting transcriptome will serve as an important broad-scale genomic resource for further studying the response of local population of L. burdigalensis to T. polycolpus pressures.