The lake area in the middle and lower reaches of the Yangtze River represents a significant concentration of freshwater lakes in China, with its biodiversity facing considerable challenges stemming from prolonged river-lake disconnection. While previous research has examined the impacts of river-lake disconnection on aquatic biodiversity, there remains a dearth of studies focusing on the taxonomic distinctness diversity of mollusk communities over long-term scales. To address this gap, this study selected seven representative lakes (comprising five disconnected lakes and two remaining connected lakes) in the middle and lower reaches of the Yangtze River, to investigate changes in the taxonomic distinctness indices of mollusk communities by comparing data from historical and contemporary periods. The findings revealed a notable decline in total species richness (from 152 to 83 species), with the average species richness decreasing from 57.7 to 30.1 (a 47.8% reduction). From the historical period to current period, the average taxonomic distinctness Δ+ and variation in taxonomic distinctness Λ+ of entire mollusks, gastropods and bivalves all remained relatively stable, except for a significant increase in the Δ+ of gastropods. Compared to the two connected lakes, the five disconnected lakes exhibited more pronounced changes in Δ+ and Λ+ indices: the Δ+ of entire mollusks (t = -3.551，p = 0.024) and gastropods (t = -2.774，p = 0.050) both significantly increased over time,while the Λ+ of entire mollusks significantly decreased(t = 2.297，p = 0.083). Additionally, in the funnel plot analysis based on the Δ+ and Λ+ indices, the disconnected lakes were predominantly located within the 95% confidence interval, while the connected lakes fell outside this range. The increase in Δ+ and decrease in Λ+ observed in mollusk communities across the five disconnected lakes were primarily driven by the significant loss of congeneric and endemic species (such as with the genera Sinotaia,Cipangopaludina,Lamprotula,and Aculamprotula). Such loss of these congeneric endemic species from the families Viviparidae and Unionidae should be regarded as a critical warning signal of biodiversity decline caused by river-lake disconnection. The findings provide scientific basis for the management and conservation of mollusk resources and diversity,as well as the ecological restoration of lakes in the middle and lower reaches of the Yangtze River under the background of river-lake disconnection.