Engineered nanoparticles (ENPs) are increasingly used to generate innovative industrial and medical goods. Because of their broad applications, they form a new class of pollutants with potential eco-toxicological impacts on marine ecosystems. Attempting to evaluate the risk, we investigated the toxicity of Iron and Zinc oxide ENPs on Paracentrotus lividus sea urchin embryos. Sea urchin embryos are sensitive to both ENPs with a much stronger impact of ZnO ENPs. Transcriptome-wide analyses were conducted after exposure to ENPs or the corresponding ions. Only a very limited number of genes are differentially expressed in response to Fe2O3 ENPs or FeCl3. In contrast, both ZnO ENPs and ZnSO4 caused alteration of biological processes with stronger perturbation of gene expression for the ionic form (higher LFC). Comparison of GO term enrichment of the differentially expressed genes indicated that ENP and ions elicited partly different mechanisms, suggesting that a nanoparticule-dependent response was induced. Remarkably, the expression of the metal binding and ROS scavenging Metallothioneins were massively induced by ZnO ENPs and ZnSO4 while ZnO ENPs and ions mainly repressed the transcription regulation processes which control embryo development. Overall design: mRNA profiles of 24h post-fertilization control or treated embryos were generated by deep sequencing, using Illumina HiSeq 2500