Pyrrhoderma noxium (Corner) L.W. Zhou & Y.C. Dai, comb. nov. (formerly known as Phellinus noxius) is a destructive root decay pathogen that affects a wide variety of host trees in pan-tropical areas, including Asia, Oceania, and Africa. The ability of P. noxium to infect a broad host range implies a dynamic pathogenicity strategy that warrants investigation of gene expression related to pathogenic lifestyle, such as genes associated with plant cell wall degradation. The genome of P. noxium (isolate P919-02W.7 from Pohnpei State, Federated States of Micronesia) was sequenced and the gene expression profile was analyzed using different host wood substrates [ponderosa pine (Pinus ponderosa), mahaleb cherry (Prunus mahaleb), black willow (Salix nigra), and sugar maple (Acer saccharum)]. The assembled genome was 33.9Mbp and 2,954 contigs and contained 9,389 predicted genes. Only minor differences were observed in size and gene content in comparison with other P. noxium genome assemblies. Transcriptome analysis revealed 488 enzymes related to carbohydrate metabolism, many of which degrade plant cell wall components. This study provides the second annotated genome of P. noxium and highlights the vast suite of decomposing enzymes of P. noxium, which suggest a potential for degrading wood from diverse host trees. This information contributes to our understanding of pathogen ecology and lifestyle.