Fish consumption is one of the major ways through which humans receive exposure to mercury (Hg). The existing forms of Hg in food, particularly Hg bound to proteins, may affect the absorption of Hg by humans and subsequently its potentially toxic effects. However, the knowledge regarding Hg-binding proteins in edible fish muscle is scarce. In the present study, salmon and tuna fish muscles, collected from seven different regions and countries, were analyzed using metallomics- and proteomics-based techniques. The concentration of Hg in sashimi samples ranged from 4.4 to 317.4 ng/g. Size exclusion chromatography (SEC) coupled with inductively coupled plasma mass spectrometer (ICP-MS) showed that beta-actin was a novel Hg-binding protein from the fish muscles, and this protein could also bind bismuth (Bi), silver (Ag), and copper (Cu). Hg bound to beta-actin accounted for approximately 30.2–37.6% of the total Hg in the tuna muscles and was significantly correlated to total Hg in the fish muscles (r = 0.98, p < 0.01) and in the fraction of soluble proteins (r = 0.94, p < 0.01). These findings suggest that proteins act as the main Hg accumulation sites in edible fish; thus, increasing human exposure to Hg following gastrointestinal digestion.