|Phellinus noxius (Corner) Cunningham causes brown root rot in a wide variety of tree species, including many plantation and landscape trees such as Cinnamomum camphora, Delonix regia, Ficus microcarpa, and Koelreuteria henryi. While infecting the trees, the pathogen not only disintegrates the bark and wood structure, but also seriously impairs nutrient transportation and water uptake, thereby causing disease symptoms such as branch dieback, yellowing and wilting of leaves, slow plant growth, and even plant death. Sometimes, the diseased trees may die within a few months of infection. Because of the severe loss it caused in Taiwan, P. noxius has attracted much attention in recent years. To analyze the genetic diversity of P. noxius, we developed a inter-simple sequence repeat (ISSR) genotyping platform based on 9 primers, with most of the ISSR banding patterns remain stable for at least five successive generations of single-arthrospore subcultures. Phylogenetic analysis of the ISSR genotypes indicated that P. noxius basidiospore isolates from a single basidiocarp form a cluster distinct from those originated from other basidiocarps. Moreover, 11 clonal lineages were identified for P. noxius isolates collected from 28 infected trees in two campuses of Taipei, which indicate the absence of any predominant virulent strain in these areas. Nonetheless, fungal isolates obtained from infected trees nearby each other tend to display similar genotypes. These results support dissemination of P. noxius through root contact and highlight the possibility of basidiospores as potential inoculum.