Introduction While the literature is replete with studies of the toxic potency of pentachlorophenol (PCP), site-specific criteria for native aquatic species that can be used in ecological risk assessments has been lacking and application of toxicity information for non-native species is controversial. Materials and methods In the present study, acute and chronic toxicities of PCP to six aquatic species native to the Yangtze River were determined. The HC 5 and HC 50 (hazardous concentration for 5% and 50% of species) were derived from dose-response curves for these native aquatic species and were then compared with those derived for non-native species. Results The acute toxicity values for the native species ranged from 8.8×10−2 mg l −1 (Plagiognathops microlepis) to 1.1 mg l −1 (Soirodela polyrhiza), while chronic toxicity values based on no observed effect concentrations (NOECs) ranged from 0.01 mg l −1 (Macrobrachium superbum) to 0.25 mg l −1 (Soirodela polyrhiza). Native aquatic benthos was more sensitive to acute PCP exposure than non-native species. There was no significant difference in NOECs derived from native fish species and those based on nonnative fish species. The median acute HC 5 and HC 50 derived from the toxicity data of native taxa were both less than those derived from non-native taxa. There was no significant difference between chronic HC 5 s derived from the two sets of taxa. However, the median chronic HC 50 derived from native taxa was less than that derived from non-native taxa.Conclusion The study upon which we report here provides site-specific toxicity information developed for native species which can be used for the protection of local aquatic life from a common contaminant, PCP.