The expression profiling of mycelium and primordium of Grifola frondosa was analyzed with high-throughput sequencing technology based on the Illumina Genome Analyzer platform.Totally 35788532 and 32755254 clean reads from mycelium and primordium libraries were obtained.Analysis of differentially expressed genes shows that there are 4094 genes differentially expressed between two libraries, and in the primordium library, 1886 of them are up-regulated while 2208 of them are down-regulated.There are 284 genes that are only expressed in the primordium library.With Blastnr comparison, genes differently expressed between two libraries are found to be related to acid protease and lectin, cytochrome, NADPH-P450 reductase, esterase, amine oxidase, clavaminate synthase, glycoside hydrolase.Genes only expressed in the primordium are found to be related to glucose, lipid, nucleic acids metabolism and cell and chloroplast membrane structure.Gene ontology functional enrichment analysis reveals that most genes related to mitochondrial membrane, glutamine family amino acid metabolic process, fatty acid biosynthetic process are up-regulated.Pathway enrichment analysis shows that genes related to ribosome are all up-regulated, and this indicates that when primordium is developed the cell metabolism speeds up and the protein synthesis increases.