In this study, a transcriptomic approach was used to evaluate the biological processes involved in the response of the photosynthetic diatom Nitzschia palea (Kützing) W.Smith (N.palea) exposed to carbon nanoparticles. The aim of this work was to determine the molecular response of diatoms exposed to low carbon nanoparticles concentration, close to potential future environmental condition, and high carbon nanoparticles concentration, representative of an accidental release. The toxicity mechanisms induced in shading and direct contact exposure were also compared. After 48h of exposure, mRNA was sequenced and a transcriptome of N. palea was generated for the first time. Significant functional annotation of the identified differential expressed genes was discussed.