Abstract: Eurotium cristatum is the dominant microorganism in dark tea,which has different sexual and asexual reproduction types.The aim of this study is to analyze the differences in gene expression between two reproductive types of Eurotium cristatum,and to provide data for the study of its reproductive development.Transcriptome sequencing was performed on the sexual and asexual strains of Eurotium cristatum to analyze the genes related to the two reproduction types and their expression mechanisms.The results showed that a total of 3 810 differentially expressed genes were found in the transcriptome sequences of the two types of hyphae,which were mainly enriched in secondary metabolites,bio-membrane,amino acid biosynthesis,and other related metabolic pathways,and were responsible for the regulation of redox reaction,catalytic activity,metal ion binding,and transmembrane transport,among others.Performed functional analyses on differentially expressed genes to screen 66 genes that might be influential in regulating Eurotium cristatum reproduction,e.g.,chsD,chsC,HOP1,DMC1,MAT1-2 and wetA,which mainly manifest their functions during spore wall synthesis,gender differentiation and calcium ion metabolic pathway.Among them,MAT1-2 and wetA have been proved to play an important role in Eurotium cristatum’ s gender differentiation and sporulation.This study can serve as a fundamental reference for the regulation of Eurotium cristatum reproduction and highly-yield fermentation procedure for sporulation.