Abstract: The hybridization of Lilium Oriental hybrids and wild lily of Sect. Sinomartagon Comber is the farmost genetic relationship and it's difficult to achieve. Researching the different expression genes in pistil of cross-compatibility and cross-incompatibility may explain the mechanism of causing orientated growth of pollen tube and the molecular mechanism of incompatible hybridization, and provide the basis for overcoming cross-incompatibility. We constructed a forward suppression subtractive hybridization (SSH) library by using the cross-incompatible Lilium Oriental hybrid pistils as the tester, and the cross-compatible ones as the driver. 180 positive clones were randomly screened out. Through sequencing, deleting the bad, removing the redundant and aligning the sequences, 113 ESTs were found to be homologous with known sequences in the bioinformatics databases. RT-PCR was performed to test the 10 selected different expression genes, which showed 1 gene was up-regulated, 7 genes were down-regulated and 2 genes were almost unchanged. Gene annotation and functional category analysis showed that the different expression genes mainly contained signal transduction(including PP2A-3, CDPK and small GTP-binding protein), transport-related(including clpB and CAT2), stress/defense(including ATPase and pyrophosphatase proton pump), protein fate related genes(including 60S ribosomal protein). It was speculated that the incompatibility in the section cross of Oriental hybrids ×Lilium pumilum was probably resulted from the abnormal signal communication between pistils and pollens, the deduced substance transport ability in pistils, the weaker stress resistance ability in pistils after incompatible hybridization.