In this study, biodiversity patterns of free-living marine nematode communities were assessed in the Yangtze River estuary and its adjacent waters by certain diversity measures. The studied area exhibited spatial variation in nematode biodiversity patterns. According to habitat heterogeneity, two station groups, shallow water near shore area and shallow water continental shelf area, were observed in the Yangtze River estuary and its adjacent waters. In general, nematode abundance and species diversity in the near shore area were significantly lower than the continental shelf area. Salinity, sediment Chlorophyll-a (Chl-a) and Phaeophytin-a (Phaeo-a) concentrations were responsible for the discrimination of species diversity measures. They reflect the reverin influence to nematode species diversity. By contrast, our results showed that the average taxonomic distinctness with presence/absence data (Δ+), and the variation in taxonomic distinctness (Λ+) were not influenced by natural environmental variability, nor pollutant and anthropogenic disturbances. The funnel plots for Δ+ and Λ+ also indicate none of the studied stations were subjected to environmental stress and perturbation. Possibly because of nematodes' strong resistance to environmental stress, the taxonomic indices did not discriminate perturbed from unperturbed conditions in the present study. We should be cautious to regard the taxonomic distinctness indices as surrogates for other traditional indices such as the number of species or Shannon diversity.