Objective In order to get genetic markers,an auxotrophic paclitaxel-producing fungus named Pestalotiopsis malicola N8 strain was isolated by genetic modification.Methods Based on the homologous recombination,URA-3 which is the key gene for uracil synthetic route of Pestalotiopsis malicola N8 strain was knocked out.The transformants were screened by minimal medium with the combination of 5-fluoroorotic acid (5-FOA) and uracil.Results The results showed that the uracil auxotrophic strain was able to grow in the minimal medium containing 5-FOA and uracil while the wild type strain was not.Conclusions The uracil auxotrophic strain can be used as a new selection marker for future gene function studies of N8 strain. Key words: Paclitaxel-producing fungus; URA-3; Gene knock-out