Abstract: The purpose of this study was to explore massive lilium’s pistil specially expressed genes and offer supports for explaining the molecular mechanism of lilium’s cross barriers. Based on the Illumina highthrough sequencing platform, the transcriptome sequencing of Lilium’s mature unpollinated pistils was conducted, the dates were assembled and the metabolism pathways were analyzed. 40792 and 39708 Unigene were disclosed in the“dry stigma”pistils LoP1 and the“wet stigma”pistils LoP2 respectively. A total of 44175 All-Unigene were generated by means of assembling sequence, removing the redundancy and clustering homologous transcripts between the two samples. 30343, 21647, 21281, 19274, 12964 and 22227 Unigene were respectively matched to the NR, NT, Swiss-Prot, GO, KEGG and COG databases via similarity alignment (E- value≤10- 5). By KEGG analysis, 19274 All- Unigene were annotated in the 128 metabolism pathways. Based on the genes analysis, it was indicated that something such as substance, energy, signal transduction and pathogen resistance had been ready for pollination and fertilization process in the mature unpollinated pistils.