Mercury is a major issue in environmental health, as it can be biotransformed to methylmercury, accumulate into aquatic organisms, and enter the food chain. Therefore, we searched for molecular markers for methylmercury exposure comparing, by differential display, exposed Xenopus embryos to controls. We found two genes whose expression is completely inhibited by CH3HgCl, and we propose them as biomarkers of exposure. The first transcript appears to be a novel gene, with a short region similar to the human iron-sulfur subunit of succinate dehydrogenase. The second gene presents a high similarity with the human homeodomain-interacting protein kinase 3 (HIPK3), a protein that is known to be involved in the apoptotic signaling pathway. These molecular biomarkers could be used to detect very early effects of the metal; furthermore, they could be useful in understanding the molecular mechanisms of mercury toxicity.