Based on the published literatures about fish assemblages in Lake Honghu, we measured the long-term changes in two taxonomic diversity indices (average taxonomic distinctness, Δ⁺ and variation in taxonomic distinctness, Λ⁺) at five periods (1959, 1964, 1981, 1993, 2004) during the half past century. The results showed that the numbers of species and genera declined from 1981, whereas the numbers of families and higher taxa decreased from 1993. Non-metric multidimensional scaling analysis based on species composition led to a separation of two groups, one grouping 1959, 1964 and 1981, the other gathering 1993 and 2004. Taxonomic distinctness indices displayed a first increase and subsequent decrease of Δ⁺, and a consistent increase of Λ⁺ through time. The five periods all fell within the 95% confidence interval for Δ⁺, but 1993 and 2004 fell significantly above the confidence interval for Λ⁺, indicating a higher unevenness of the distribution of taxa across the taxonomic tree than random expectations. Δ⁺ and Λ⁺ could provide complementary information about the variability of biodiversity in addition to traditional diversity indices, thus we proposed that taxonomic distinctness indices can be used as promising tools in studies of biodiversity and environmental assessment.