The Yangtze River (6,380 km long) is the longest river in Asia and the third-longest one in the world. Its river basin (a complex riverine–lacustrine network) is especially rich in fish fauna, representing high species richness and endemism, and therefore is a globally significant area for preserving fish biodiversity (Dudgeon 2000; Park et al. 2003). However, during the past several decades, loss of fish biodiversity in the Yangtze River Basin has been accelerated by a series of direct and indirect effects of human activities and environmental changes, e.g., disappearance, shrinkage, and fragmentation of habitats for fish spawning, feeding and migration, overfishing, water pollution, and invasion of exotic species (Zeng 1990; Xie and Chen 1999). Despite numerous publications on ichthyological research in the Yangtze River Basin since the 1950s, synthesis and analysis or assessment of fish distribution patterns and quantification of major threats to fishes are still limited, which in turn limits formulation of biodiversity conservation strategies. In this study, we collected and synthesized the scattered data from relevant literature, with the purposes of (1) assessing large-scale distribution and endemic species composition of Yangtze fishes, (2) ranking the contribution of major threats as well as intrinsic factors to fish endangerment, and (3) providing recommendations for fish conservation in the basin. The Yangtze River Basin consists of five defined areas (Fig. 1). The riverhead is located on the Tibetan Plateau, where the mean elevation is over 4,500 m (Zeng 1990). The upper reach extends upstream from Yichang (in Hubei Province), with a length of more than 4,300 km and a drainage basin area of 100 9 10 km. The Yangtze flows primarily across mountainous regions with steep channel slopes of 10–40 9 10 (Chen et al. 2001). The famous Three Gorges Dam is located in the upper mainstream. The middle reach lies between Yichang and Hukou (in Jiangxi Province), with a length of about 950 km and a drainage area of 68 9 10 km. Low relief topography with channel slopes of 2–3 9 10 and meandering platforms are characteristics of this region. Here, the river connects with shallow lakes of various sizes and numerous tributaries and forms an endemic Chinese compound ecosystem of inland water. The lower reach extends from Hukou downward to the mouth of the river, with a length of 930 km and a drainage area of 12 9 10 km. This segment of the river wanders among plains and hills with lower channel slopes of 0.5–1.0 9 10. Several large interior lakes, such as Lake Caohu and Lake Taihu in association with many tributaries, drain into the reach (Chen et al. 2001). The river empties into the East China Sea at the estuary, which is characterized by three bifurcations and four outlets into the sea and a complicated temporal and spatial salinity distribution (Mao et al. 2001). Fish taxonomy and distribution in the five defined basin areas were compiled from scattered published fish surveys since the 1950s. To ensure data quality and authenticity, faunal compositions derived from extensive surveying and/ or long-term monitoring were adopted. The used literatures include Chu (1955), Anonymous (1976, 1980), Yang (1987), Zeng (1990), Wu and Wu (1992), Ding (1994), Chen (1998), Chu et al. (1999), Yue (2000), Ni and Zhu (2005), Zhuang et al. (2006), and Wu and Zhong (2008). Endemic species were defined according to their distribution being limited to the Yangtze River Basin. Patterns of distribution range of the fishes were indicated by the S. Ye (&) Z. Li T. Zhang J. Liu S. Xie State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P. R. China e-mail: yeshw@ihb.ac.cn