The mycelium and yeast-like cells of Tremella fuciformis were adopted to construct transcriptome sequencing library by RNA-Seq. 13.16 G data and 16 190 Unigene were generated from de novo splicing. Among the Nr database annotated Unigene, 55.75% and 13.35% of them had similar sequence to T. mesenterica and Cryptococcus neoformans, respectively. 7 203 Unigenes were annotated in the COG database, which could be divided into 25 terms. 3 921 Unigene were annotated in the GO database, and divided into 3 major categories and 46 branches. From the KEGG analysis, differential expressed genes were enriched in pathways, including the metabolism of amino and nucleotide, and Intracellular phase. All the results provided abundant data resource for further investigating of T. fuciformis on polysaccharides and amino acid metabolism pathways and the important genes involved in them.