Abstract: In this study, we measured the contents of heavy metals in the muscles and the livers of Coreius heterodon and C. guichenoti of different ages in the upper-, middle-, and down-streams of the Three Gorges Reservoir (TGR). We aimed to clarify the current situation of heavy metal pollutions in the native species in the TGR, and to assess the potential risks in the fish ecosystem and food safety. The concentrations of Mercury (Hg), arsenic (As), lead (Pb), cadmium (Cd), copper (Cu), zinc (Zn) and chromium (Cr) in the muscles and livers of fish were determined with the methods of plasma absorption spectrometry, graphite furnace atomic absorption spectrometry, and atomic fluorescence spectrometry. The concentrations in the muscles of the two fish species were Zn Cu Cr Hg AsPbCd. In the livers, the orders were Zn Cu Pb Cd Cr As Hg, and Zn Cu Pb Cr Cd Hg for C. heterodon and C. guichenoti respectively. The concentrations of heavy metals in the livers were significantly higher than that in the muscles (P0.05). Overall there was no significant difference in the concentration of each heavy metal between the individuals obtained from different locations, although there were a few exceptions. The concentrations of heavy metals in the muscles-the edible part of fishwere all under the limit according to the National Standards of Aquatic Product Safety. The concentrations of most heavy metals (except for Cd and Pb) in the livers were also in the safe range. These results uncovered the current status of heavy metal pollutions in the two indigenous economic fish species in the TGR, and contributed to better understanding of the quality and safety of the aquatic products in this area.