As an ornamental plant, Fatsia japonica has been widely used in gardens. From April 2021 to 2022, a disease that caused the wilting and root rot of F. japonica in a large area was observed, which eventually led to the plants wilting and dying, while the leaves did not fall off. This disease greatly reduced the landscape effect of plants. An oomycete species was isolated from the roots of the infected plants. This colony morphology was slightly radial to stellate, and the aerial mycelium was flocculent. Oval sporangia with papillae, apical chlamydospores and zoospores formed in sporangia were observed. The morphological characteristics were consistent with Phytophthora. For accurate identification, the internal transcribed spacer (ITS), cytochrome oxidase subunit II (COXII) and large ribosomal subunit (LSU) genes were amplified and sequenced. The species was identified as Phytophthora nicotianae using phylogenetic analysis. Finally, the disease was reproduced by inoculating healthy F. japonica with a zoospore suspension; the symptoms were consistent with those of natural infections, and the isolate obtained from artificially infected plants had the same morphological characteristics as the inoculated isolate. The results demonstrated that P. nicotianae is the pathogenic factor of root rot. of F. japonica. This is the first report of root rot on F. japonica caused by P. nicotianae in China.