Laboratory trials have suggested that plastic particles Procambarus clarkii, Girard, 1852) is an alien species able to tolerate highly perturbed environments. As benthic detrivore, this species can be susceptible to plastic ingestion. Ten adult specimens of P. clarkii, at intermolt stage, were individually exposed to 100 µg of 100 nm anionic carboxylated polystyrene nanoparticles (PS-COOH NPs) in a 72h acute toxicity test. PS-COOH NPs were embedded in an agarose-based food matrix and administered through diet. At the same time, ten control individuals were fed with agarose-food without NPs. An integrated approach has been conceived to assess the biological effects of nanoplastics, by analysing both transcriptomic and physiological responses. Total haemocyte counts, basal and total phenoloxidase activities, glycemia and total protein concentration were investigated in crayfish haemolymph at 0h, 24h, 48h and 72h to evaluate general stress response over time. Transcriptomes of hemocytes and hepatopancreas have been analyzed to ascertain differentially expressed genes (DEGs) in response to PS-COOH NPs-challenge after 72h. While physiological assays did not show substantial alterations between treated and control groups, the RNA-seq analysis revealed few key differentially expressed genes (DEGs). A total of 12, 98 and 32 DEGs were identified in the hemocytes, female and male hepatopancreas, respectively. Interestingly, genes involved in cell-mediated innate immune responses were up-regulated in the hemocytes. In digestive glands, PS-COOH NPs exposure was related to the down-regulation of genes involved in the lipid metabolism in females and the up-regulation of haemocyanin genes in males. This study suggest that a low concentration of PS-COOH NPs exposure may induce light stress in crayfish.