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Wilsonomyces carpophilus is a necrotrophic plant pathogenic fungus with a wide host range infecting all stone fruits such as peach, plum, apricot and cherry, and almonds among the nut crops. Necrotrophs are more devastating with a complex pathogenicity mechanism and least known effector repositories. Here, we report a 29.9 megabase draft genome assembly of W. carpophilus. We explored the hybrid technology of Illumina HiSeq and PacBio sequencing technologies to get the unbiased results of sequence reads. We aligned short Illumina reads against the long PacBio reads. A total of 10,901 protein-coding genes were predicted that includes varied set of genes such as HET genes, cytochrome-p450 genes, kinases etc. We mined 2851 simple sequence repeats (SSRs) in the genome assembly. We also predicted the diverse inventory of secretory proteins, transporters, primary and secondary metabolic enzymes. A total of 225 secreted proteins, hydrolases, polysaccharide-degrading enzymes, esterolytic, lipolytic and proteolytic enzymes were the most significant proteins reflecting the necrotrophic lifestyle of the W. carpophilus. We also identified 146 tRNAs and 52 rRNAs in the pathogen genome.