This study focused on characterizing the endemic fish assemblages in the upper Yangtze River Basin and identifying the relative influences of catchment land-cover variables on observed fish patterns in order to suggest a conservation strategy. A model based on a self-organizing map was applied to determine endemic fish assemblages along the river network, based on presence/absence data for 124 endemic species. Five fish assemblages (Ia, Ib, IIa, IIb1, IIb2) were described. These assemblages varied significantly in terms of individual species patterns as well as species richness. Indicator species were identified for each class of community (0, 3, 9, 27, 0 species for cluster Ia, Ib, IIa, IIb1, IIb2, respectively). Structure of the endemic fish assemblages in the upper Yangtze River was highly correlated with local topographic and geomorphic characteristics. Simultaneously, the catchment land cover features also reflected out this endemic fish distribution structure. Among 18 land-cover types, alpine and sub-alpine meadow, together with farmland, were revealed to be the most important factors both in discriminating the endemic fish assemblages and in correlating species distributions by using discriminant analysis and co-inertia analysis. Finally, in order to preserve the rare and endemic fish in the upper Yangtze River, reserve networks, rather than a single national nature reserve, should be established.