The transcriptome of Monascus growth under cheese matrix environment was analyzed by RNA-Seq technology.Using second generation sequencing technology,based on the analysis of Illumina NextSeq 500 sequencing platform,the transcripts with 59 935 140 bp and unigene with 22 377 414 bp were obtained (total 18 042).The Unigene obtained by clustering was compared with NR,GO,KEGG,eggNOG and Swiss-Prot databases and annotated with gene function.The GO,eggNOG and KEGG database was annotated to 12 186,17 777 and 3 251 sequences,respectively.42 pathways were obtained.The completion of these annotations information provided basis for the application of Monascus in the cheese production.