Phellinus species are basidiomycete fungi that are widely distributed tropical and sub-tropical regions of the world. In particular, Phellinus noxius causes brown root rot disease in 200+ known tree species. Originally played a role of replacing old trees in natural forests, they have recently have emerged to be problems to greater disease foci in forests, monoculture plantations and amenity trees in urban cities. We produced a 12 piece 31.6Mb genome assembly from a Japanese Phellinus noxius KPN-91 isolate using long read sequencing, as well as draft assemblies from three other members of Hymenochaetaceae. Repeat induced mutations are apparent in the genomes of these species, with greater than 40kb transposable element clusters indicative of centromeres. P. noxius genome presents itself with little variability in gene density, simple repeat density or conserved genes along its scaffolds, with the exception of expansion of nucleotide-binding oligomerization domain (NOD)-like receptors (NLRs). Interestingly, degraded mesosynteny are observed between P. noxius and C. coprinopsis, suggesting karyotype conservation are still conserved in basidiomycetes. Sequencing of 61 isolates of P. noxius collected in Japan and Taiwan over 2012-2016 period reveals a single population with exceptionally high diversity at synonymous sites of 0.15. Transcriptome comparisons between P. noxius fungal mats of infected trees against fruiting bodies reveal upregulated genes involved in trehalose biosynthetic pathway which has been implicated in infectivity by fungal pathogens. The Hymenochaetales are phylogenetically placed between the better-studied Polyporales/Agaricales and Tremellales/Ustillaginales orders, making the small assembly of P. noxius an attractive genome to study the evolutionary transition between these orders of Basidiomycota.