Background: Mercury (Hg) is a globally ubiquitous pollutant and one of the most dangerous metal contaminants, which presents a high risk of bioaccumulation in living organisms. In this study, we mapped the distribution of Hg and other trace elements in zebrafish (Danio rerio), which were exposed to mercury (II) chloride in order to assess its toxicity, bioaccumulation and distribution in fish organs. Methods: Adult zebrafish were exposed for 7 days to different concentrations of mercury (II) chloride and the elemental distribution was obtained through the micro-energy dispersive X-ray fluorescence technique (μ-EDXRF). Results: The results showed that Hg levels, measured in fish tissues, were indicative of bioaccumulation within some of its organs (e.g. visceral mass, gills), and that the physiological processes of accumulation were highly dose-dependent. In addition, the results showed higher concentrations of Hg in the gills. Moreover, other trace elements (e.g. Fe, Cu and Zn) levels were not altered after fish exposure to mercury(II) chloride. Conclusion: The μ-EDXRF results were assessed along with the determination of some oxidative stress biomarkers (e.g. antioxidant enzymes) to understand the effects behind the Hg bioaccumulation and toxicity. These results suggest that the metabolic changes in zebrafish due to the exposure to Hg are consistent with oxidative stress.