Fish is an important concentrator of mono-methyl mercury and the main route to human contamination. We compared fish Hg bioaccumulation (within similar weight ranges) in two Amazonian river habitats during high-water seasons. The Rio Madeira has been greatly impacted by agriculture, alluvial gold extraction, and a hydroelectric reservoir, whereas the Rio Negro is much less affected by these human activities. The species at the top of the food web, Hoplias malabaricus (piscivorous; 80-668 ng Hg/g) and Cichla spp. (piscivorous; 42-747 ng Hg/g) showed the highest range of Hg concentrations. Nonpiscivorous species with comparable weight range, such as Potamorhina latior (detritivorous; 20-157 ng Hg/g) and Myleus torquatus (herbivorous; 2-182 ng Hg/g), had lower Hg concentrations. Triportheus elongatus (omnivorous; 5-350 ng Hg/g), with the lowest weight range, also showed a low range of Hg concentrations. Despite the Rio Madeira's higher sediment load as well as environmental impacts (deforestation, agriculture, hydroelectric reservoir, and alluvial gold mining) on natural Hg release, fish Hg bioaccumulation was no different between the two river habitats for nonpiscivorous species. In this small observational study only the species at the top of the food web (M. torquatus, Cichla spp, T. elongatus) showed higher mean Hg concentrations in the Rio Madeira than the dominantly wilderness habitat of the Rio Negro.