Mercury still represents one of the most hazardous threats for the aquatic ecosystem due to its high toxicity, and the fact that it can be easily incorporated into the food chain by accumulation in fish as MeHg. On the other hand, selenium is a micronutrient that is part of different antioxidant enzymes that regulate the cellular redox state, and whose complex interaction with Hg has been extensively studied from a toxicological point of view. In order to evaluate the protective effect of Se(IV) co-administration against MeHg accumulation and toxicity, we have selected an in-vivo model at two developmental stages: zebrafish eleutheroembryos and adult fish. Embryos were exposed during 48 h to MeHg (5 or 25 μg/l) and a concentration of Se (IV) representing a molar ratio close to one (2.5 or 12.5 μg/l), while adult zebrafish were exposed during 72 h to either 25 μg/l of MeHg alone or co-exposed with 12.5 μg/l of Se (IV). A significant decrease in MeHg bioaccumulation factor was observed in eleutheroembryos co-exposed to Se(IV). A time-dependent accumulation of MeHg was observed in all the analyzed organs and tissues of adult fish, which was significantly reduced in the muscular tissue and the intestine by Se(IV) co-administration. However, such protection against MeHg bioaccumulation was not maintained in the brain and liver. The data derived from the gene expression analysis also demonstrated the protective effect of Se(IV) against MeHg-induced oxidative stress and the activation of different defense mechanisms by Se(IV) co-administration.