In the frame of in vitro eco-toxicological studies we performed a transcriptomic analysis by ncounter Nanostring technology in order to assess the molecular effects of different stressors (physical, biochemical, chemical) on embryos and adult immune cells of the Mediterranean sea urchin species Paracentrotus lividus, used as model organism as very sensitive to chemical and physical environmental changes. By in silico analysis we chose a probe set of sequences targeting 130 genes, encoding for growth and transcription factors, structural proteins, stress and immune response proteins. For this aim, we retrieved the most of the sequences from the NCBI nucleotide database and in addition, identified, sequenced and characterized some new transcripts of P. lividus.