Abstract: Illumina HiSeq2000，a high-through transcriptome sequencing technology，was applied to obtain the transcriptome differential expression data of stigma after self-pollinated 30 min，cross-pollinated 30 min and unpollinated. The objective of this study is to analyze the differences of gene expression of stigma after self-pollination and cross-pollination in Brassica oleracea L. var. capitata，and further analyze the significantly different expression genes. Transcriptome sequencing obtains a total of 2.38 × 1010 bp bases containing 1.6 × 108 of the original pair-end reads. There were 2 900 and 2 328 genes with altered expression in stigma after self-pollination and cross-pollination in Brassica oleracea L. var. capitata，respectively，and a total of 1 904 common genes expressed between two samples. The greater proportional difference after self-pollination is cell killing，extracellular matrix part and nucleic acid binding transcription factor activity. The greater proportional difference after cross-pollination is the signaling，extracellular region part，nutrient reservoir activity and structural molecule activity in the background of differential expression genes and all genes. GO enrichment analysis illustrated that the 40 specific highly significant GO terms in self-pollination sample mainly involved in sugar transmembrane transporter activity，tubulin binding and calmodulin-dependent protein kinase activity. The 53 specific highly significant GO terms in cross-pollination sample mainly involved in farnesoic acid O-methyltransferase activity，minus-end-directed microtubule motor activity and auxin influx transmembrane transporter activity. About 563 and 453 genes their expression was significantly up-regulated and down-regulated respectively in the 996 specific differentially expressed genes in self-pollination sample，which mainly related to calciumion binding，cytoskeletal correlation，jasmonic acid mediated signalin0g pathway and salicylic acid mediated signaling pathway. The 424 specific differentially expressed genes in cross-pollination sample mainly involved in transmembrane transport of substance and lipid metabolism．

Key words: Brassica oleracea L.var. capitata, self-incompatibility, transcriptome, differentially expressed gene