Selenium and total and organic mercury were determined in the liver and kidney of franciscana dolphin (Pontoporia blainvillei) incidentally caught in fishing nets along two Brazilian coastal areas (southeast and south). Regional differences in the concentrations of these contaminants were observed in P. blainvillei. Liver showed the highest organic and total mercury. In general, samples of individuals collected at the southern of Brazil had the highest concentrations of selenium and total and organic mercury. No significant gender differences were observed. Growth stage influenced the accumulation of these contaminants in both organs, and hepatic concentrations increased with the body length, according to the sampling area. Molar mercury and selenium concentrations in liver were significantly correlated, with a Se:Hg ratio close to 4. The among-site differences we found may be related to differences in preferred prey, bioavailability in the marine environment, environmental conditions, or these individuals may belong to distinct populations.