Nanoparticles are a newly emerging class of pollutants with eco-toxicological impacts on marine ecosystems; they are characterized by nano-scale size which improves their physical, chemical and biological properties. To better understand the mechanisms of embryotoxicity of carbon-based nanoparticles, the genotoxicity and the perturbation of the Gene Regulatory Network (GRN) expression have been investigated during the development of the sea urchin Paracentrotus lividus from fertilization to early pluteus stage. Increasing quantities of carbon nanoparticles (C-NPs), 0.5, 2.5 and 25 × 1013 C-NPs/500 cm3 of filtered seawater were administered during fertilization and the development was monitored up to the early pluteus stage (48 h). DNA damage and gene expression were assayed by Comet assay and Real-Time PCR, respectively. Taken together, our results indicate that embryo malformations taking place in the presence of C-NPs are due to altered regulation of the GNR and to a progressive accumulation of DNA single-strand breaks.