Abstract: In the middle-lower reach of the Yangtze River, there are many lakes with intensive fish biodiversity, which are connected with the Yangtze mainstream historically. Since the 1950s, most of these lakes have experienced river-lake disconnection by anthropogenic impacts, leading to remarkable biodiversity decline of fish in these lakes. Based on the published literatures about fish assemblages in lakes, the taxonomic distinctness and temporal changes of fish communities in the connected lakes and disconnected lakes were examined by using two taxonomic diversity indices (average taxonomic distinctness, Δ⁺ and variation in taxonomic distinctness, Λ⁺), to assess the impact of river-lake disconnection. The results indicated that disconnected lakes showed significantly lower species richness and Δ⁺ values (average values of 48.47±14.64 and 74.02±3.093, respectively) than connected lakes (average values of 76.22±14.40 and 78.31±0.98, respectively; P<0.001), indicating the loss of fish diversity. On the contrary, the disconnected lakes showed significantly higher Λ⁺ values (average values 736.89±33.80) than connected lakes (average values of 697.31±25.53; P=0.002), indicating the increasing unevenness of taxonomic distinctness. Our analysis of temporal changes showed that species richness and Δ⁺ generally declined, and Λ⁺ generally increased through time within representative connected and disconnected lakes. However, the species richness, Δ⁺ and Λ⁺ values of the connected lake fluctuated over time, and the Λ⁺ increased significantly over time. These mean that connected lakes were also affected by various disturbances, which led to the decline of taxonomic diversity and the distribution of fish in disconnected lakes was more concentrated in some taxa resulting high unevenness and low stability in the community. Based on our results, we suggested to restore the fish diversity in the middle and lower reaches of the Yangtze River by recovering the connection between the lakes and the Yangtze mainstream, improving the quality of fish habitat through water environment management, and scientifically adjusting the fish community structure.