Highly toxic compounds, as petroleum and its derivatives, solvents, alkanes, polycyclic aromatic hydrocarbons (PAHs), pesticides, fertilizers, and heavy metals, released constantly in the environment due to industrial and agricultural activities, are often highly persistent and accumulate in the environment. Several strategies have been studied to remediate polluted environments, based on physical, chemical, or biological methods (Bioremediation). Well known bioremediation agents include plants and microorganisms, as well as their metabolites and enzymes. They have the potential to be exploited in biotechnological application for bioremediation in a broad range of habitats and conditions. Associations between diverse organisms may improve results significantly. Within our collection, we selected a strain of the fungus Byssochlamys nivea for its ability to grow on pentachlorophenol-contaminated soil. The use of this and other taxonomically related fungi is strongly limited by the lack of biochemical and transcriptomic data on degradation processes of recalcitrant organic pollutants. In addition, limited genomic reference data discourages investigation on structural and functional diversity allowing this species to interact with contaminants. In order to overpass the hole of sequence data to study genetic basis of diversity in B. nivea we generated a 3'-cDNA library and deeply sequenced it using a Next Generation Sequencing approach. Assembling of reads resulted in 33,000 contigs and 37% of them showed a BLAST hit in the NCBI "nonredundant protein sequence database". The provided library is expected to encourage the use of B. nivea as model specie for structural and functional investigation in genomics. Particularly, this cDNA library could benefit biotechnological approaches aimed at investigating catabolic processes involved indegradation of recalcitrant organic pollutants for development of innovative bioremediation systems