The Three Gorges region, located on the upper reaches of the Yangtze River in central China, is considered one of the most important biodiversity hotspots in China. It harbours more than 6000 plant species, over 500 terrestrial vertebrates, and about 160 species of fish. In addition to this taxonomic richness, the region is home to many endemic and threatened taxa, which may be the result of its role as a glacial refuge. The construction of the Three Gorges Dam may have serious consequences for this biodiversity. The flooding of more than 600 km2 together with massive population resettlement will involve the loss and/or fragmentation of many terrestrial habitats in the reservoir area, affecting both plant and animal species. Furthermore, negative effects on downstream terrestrial biodiversity are expected due to the regression of floodplains and riparian wetlands after the dam is completed. The alteration of river flow caused by the dam will also have a severe impact on freshwater biodiversity throughout the whole Yangtze River system, especially on migratory fish but also on other aquatic life, such as the emblematic Yangtze River dolphin. The conservation measures implemented by the authorities, although valuable, may well be insufficient to mitigate the negative effects of the dam on biodiversity.