Concentrations of copper, zinc, mercury, and arsenic were measured in the muscle, gill and liver tissues of Coreius heterodon and Pelteobagrus vachelli collected from the rare and endemic fish nature reserve in the upper reaches of the Yangtze River. The concentrations of copper and zinc in the tissues of these two fish species were higher than those of mercury and arsenic. Highest metal concentrations were generally found in fish samples from Yibin. The concentrations of copper, zinc, mercury, and arsenic in C. heterodon were higher than that in P. vachelli. The fish from this study area were not safe for human consumption.