For studying the long-term changes in taxonomic diversity (average taxonomic distinctness and variations in taxonomic distinctness) of fish community in Yangtze River estuary, fish species recorded at three periods (1985~1986, 2004, 2010~2011) were used to estimate the △+ and ∧+ for respective survey. The results showed that △+ in 2004 and 2010~2011 (except the spring survey) fell below the 95% probability limits for △+ of all fish species from Yangtze River estuary. Moreover, the decreasing trends in △+ were also observed. However, patterns of variation in ∧+ was different from △+, as all ∧+ distributed in the 95% probability limits for∧+ of all fish species. Declines in △+ of Yangtze River estuary may be a result of overfishing, pollution and habitat destruction, as shown in closer relationships among fish species, implying for increased niche similarity between species and potential loss of stability or resilience of the community.