The aim of this study is to contribute to the understanding of the mechanisms underlying nanoparticle (NP)-induced embryotoxicity in aquatic organisms. We previously demonstrated that exposure of male gametes to NPs causes non-dose-dependent skeletal damage in sea urchin (Paracentrotus lividus) larvae. In the present study, the molecular mechanisms responsible for these anomalies in sea urchin development from male gametes exposed to cobalt (Co), titanium dioxide (TiO2) and silver (Ag) NPs were investigated by histochemical, immunohistochemical and Western Blot analyses. P. lividus sperm were exposed to different NP concentrations (from 0.0001 to 1 mg/L). The distribution of molecules related to skeletogenic cell identification, including ID5 immunoreactivity (IR), wheat germ agglutinin (WGA) affinity and fibronectin (FN) IR, were investigated by confocal laser scanning microscopy at the gastrula (24 h) and pluteus (72 h) stages.Our results identified a spatial correspondence among PMCs, ID5 IR and WGA affinity sites. The altered FN pattern suggests that it is responsible for the altered skeletogenic cell migration, while the Golgi apparatus of the skeletogenic cells, denoted by their WGA affinity, shows different aspects according to the degree of anomalies caused by NP concentrations. The ID5 IR, a specific marker of skeletogenic cells in sea urchin embryos (in particular of the msp130 protein responsible for Ca2+ and Mg2+ mineralization), localized in the cellular strands prefiguring the skeletal rods in the gastrula stage and, in the pluteus stage, was visible according to the degree of mineralization of the skeleton. In conclusion, the present study suggests that the investigated NPs suspended in seawater interfere with the bio-mineralization processes in marine organisms, and the results of this study offer a new series of specific endpoints for the mechanistic understanding of NP toxicity