Abstract: Based on the genome data of Lentinula edodes, the codon preference and preference forming factors of its nuclear genomic genes were analyzed. The GC content of L. edodes nuclear coding genes was 48.66%, and the frequency of base T in the third position of synonymous codon was the highest（T3s, 36.07%）, and the contents of GC, GC3 and GC3s of highly expressed genes were significantly higher than the genome level. Correlation analysis showed that gene expression was significantly positively correlated with sequence C3s content, GC3, GC3s, GC contents, C content and CAI. The results of relative synonymous codon usage analysis showed that there were 29high-frequency codons in the coding sequence of L. edodes genome, and 16 optimal codons were identified on the basis of screening high expression and low expression genes by transcriptome. The analysis of influencing factors of preference formation showed that the formation of codon bias in L. edodes genome was affected by neutral mutation and selection pressure. This study can provide a reference for the functional analysis of key genes and the study on the mechanism of postharvest quality deterioration of L. edodes fruiting body.