The transcriptome of the fruiting body of maitake was sequenced by Illumina to study the expression profiling and predict the functional gene.63 137 Unigenes were obtained through sequence assembly,for which 46 670 Unigenes were annotated through NR database by BLAST.A total of 27 472 Unigenes were identified to correspond with 239 biological pathways by annotating and forecasting the biological pathways for the transcriptome of Maitake.There were 5 294 SSR in 63 137 Unigenes were found,which accounting for 8.38% proportion of the total number of Unigenes.The characteristic of SSR distribution showed that mono-nucleotide repeat was the highest reaching 63.4%,following by tri-nucleotide repeat,which was 24.44%.The types of SSR were analyzed that A/T was the highest repeat,following by CCG/CGG and AG/CT.