Ganoderma boninense is the dominant fungal pathogen in causing Basal Stem Rot (BSR) disease on oil palm. The whole genome of this fungus was sequenced using PacBio RS II platforms to gain the whole-genome shotgun libraries. These libraries were smoothed with Illumina Hiseq 4000 paired end sequencing to polish the genome assembly. Subsequently, a combination of Dovetail Chicago and HiC libraries with the HiRise assembly pipeline revealed the 12 pseudo-chromosomes of G. boninense. This is the first report of chromosomal-scale genome assembly for the most important fungal pathogen on oil palm.