Hypsizygus marmoreus (Peck) H.E. Bigelow is a typical white-rot fungus and is widely cultivated in China and Japan. In this study, the genome of a monokaryon strain HM26-F1 was sequenced using Illumina and Pacbio platforms. The genome sequences of 32,238,363 bp with 49.40% G+C content were obtained and 14,443 gene models coding for proteins were determined. The divergence time was 144 million years ago (MYA) and diverged from other fungi belonging to Agaricales around the late of Jurassic Period. 363 carbohydrate-active enzymes (CAZymes) genes were detected in this genome. And there were higher number of class II peroxidases (11) and multicopper oxidases (22) for degrading lignin. In addition, 418 genes were enriched involving in purine metabolism for IMP and GMP synthesis. And, there were 7 secondary metabolite clusters in the genome, including 3 terpene, 2 polyketide biosynthase, 1 nonribosomal peptide synthetase and 1 siderophore. Combining Hiseq 2500 and Pacbio platforms resulted in a more complete and less fragmented genome. H. marmoreus had high abilities to degrade lignocellulose. IMP and GMP may be the basis of the crab flavor. Information obtained from this study enhances our knowledge about degradation mechanisms of lignocellulose and secondary metabolism.