The aim of this work was to assess the relationship between mercury concentrations in the blood with that in muscle for non-invasive mercury contamination assessment in fish. At Ribeira Bay were collected 198 fishes of 4 species (Genidens genidens, Arius luniscutis, Haemulon steindachneri, Micropogonias furnieri). At Guanabara Bay were collected 84 fishes of 2 species (Genidens genidens, Micropogonias furnieri). Means of mercury concentrations in fish muscles in both areas were below 500 ng/g. The mean ratio, including all specimens of all species, for mercury in muscle-to-whole blood was 13.4:1, for muscle-to-erythrocytes, 6.5:1 and for erythrocytes-to-plasma, 6.5:1. Further studies are necessary to insure that blood could be used as an exposure biomarker, in order to assess mercury availability in aquatic ecosystems.