Ganoderma boninense, a soil born fungus, is the main agent of basal stem rot, one of the most devastating diseases of oil palm (Eleais guinensis). Observation of oil palm infection by G. boninense in natural conditions has shown the fungus capacity to quickly degrade the stem base, leading to important cracks and finally to tree fall. This important degradation of host tissue likely implies lignolitic enzymes, in particular laccase activity. Those enzymes have been well described in several rot disease involving fungus and their role in the pathogenicity of some fungus like the honey mushroom (Armillaria mellea) is well established. In this context, the study of G. boninense wood degradation genes, and in particular of laccase genes, seems to be of key interest to a better understanding of basal stem rot disease. We produced and assembled a draft sequence genome of an Indonesian G. boninense isolate and the draft sequence of a Malaysian isolate transcriptom. The draft genome assembly was annotated ab initio with Augustus software that predicts genes models from genomic sequence. We obtained 22228 gene models, among which 33 showed similarity with laccase. Among these 33 gene models, 25 exhibited the 4 domain laccase signature sequence and seven showed matches with expressed transcripts. Their length, intron number, subcellular addressing and peptide signal are classical of fungal laccases. A phylogenic analysis of G. boninense laccase predicted gene models along with other fungal laccases suggest recent and extensive gene duplication in G. boninense for a laccase clade specific to some polyporales white rot fungi.