In order to explore the molecular mechanism of the variation of kiwifruit from dioecious to monoecious， transcriptome sequencing， bioinformatics analysis and qRT-PCR verification on female and male flowers of the monoecious mutant of Mantianhong kiwifruit were carried out. The results of transcriptome differential expression gene identification showed that there were 337 differentially expressed genes （DEGs） between female and male flowers， with 241 genes up-regulated and 96 genes down-regulated in male flowers. The GO and KEGG enrichment of DEGs showed that compared with female flowers， the up-regulated genes in male flowers were mainly involved in the metabolism of amino sugars and nucleotide sugars and the synthesis of secondary metabolites. The down-regulated genes were mainly enriched in secondary metabolite synthesis， carotenoid synthesis and other pathways. Through functional annotation analysis， 30 potential gender-related regulatory genes were identified， five of which were expressed in the secondary metabolite synthesis pathway. Seven DEGs were selected for qRT-PCR， and their expression levels in male and female flowers were in accordant with those in transcriptome data. The results of this study provide a theoretical basis for the creation of kiwifruit monoecious materials.