Aims:  To characterize and identify a new taxol‐producing fungal strain HD86‐9 isolated from Taxus cuspidata in China. Methods and Results:  Taxol extracted from strain HD86‐9 was identified by HPLC and MS analyses. Strain HD86‐9 was cultured and its morphology and phenotypes were described. HD86‐9 displayed morphology most similar to that of Aspergillus niger but presented differences in the shape and size of the conidia. The growth evaluation showed that the maximal tolerable temperature of the new strain was 43°C, higher than that of the model Aspergillus niger. The 18S rDNA and the internal transcribed spacer region including the 5·8S rDNA of HD86‐9 were amplified by PCR; molecular analysis of these sequences revealed their high similarity of 98% to those of Aspergillus niger. Conclusions:  The morphology and molecular analysis identified HD86‐9 as a new variant of taxol‐producing endophytic fungi, and it was named Aspergillus niger var. taxi D.P. Zhou, K. Zhao and W.X. Ping, var. nov. Significance and Impact of the Study:  As the first report of a taxol‐producing variant of Aspergillus niger species, this study offers important information and a new resource for the production of an important anticancer drug by endofungus fermentation.