Clitopilus hobsonii (Entolomataceae, Agaricales, Basidiomycetes) is a common soil saprotroph. There is also evidence that C. hobsonii can act as a root endophyte benefiting tree growth. Here, we report the genome assembly of C. hobsonii QYL-10 isolated from ectomycorrhizal root tips of Quercus lyrata. The genome size is 36.93 Mb, consisting of 13 contigs (N50=3.3 Mb) with 49.2% GC-content. Of them, 10 contigs approached the length of intact chromosomes, and 3 had telomeres at one end only. BUSCO analysis reported a completeness score of 98.4% using the Basidiomycota_odb10. Combining ab-initio, RNA-seq data, and homology-based predictions, we identified 12,710 protein-coding genes. Approximately, 1.43 Mb of Transposable elements (TEs) (3.88% of the assembly), 36 secondary metabolite biosynthetic gene clusters and 361 genes encoding putative CAZymes were identified. This genomic resource will allow functional studies aimed to characterize the symbiotic interactions between C. hobsonii and its host trees, but will also provide a valuable foundation for further research on comparative genomics of the Entolomataceae.