Abstract:To identify the Phytophthora capsici stress induced genes of pepper, a high P.capsici resistant pepper cultivar was used as main material in this study. With cDNA from pepper seedlings treated with P.capsici as the tester and cDNA from this plant in normal growth as the driver, we constructed subtracted library using suppression subtractive hybridization (SSH). Thirty positive clones were picked out randomly from SSH library, plasmid PCR suggested that the inserts were between 200-1 000 bp and library was suitable for the following work. Forty clones were randomly selected and sequenced, 35 differential gene fragments were obtained. Blastx analysis showed that 30 ESTs have high homology with known genes in GenBank, 5 ESTs was unknown function genes. The obtained known function ESTs code NAC transcription factor protein, Serine/threonine protein kinase, cytochrome P450 monooxygenase, chlorophyll a b-binding protein, glutathione s-transferase, chitinase, respectively. These expressed genes are involved in disease-resistant signal transduction, antioxidative stress, transcriptional regulation, photosynthesis, physiological processes. The research established a basis for cloning stress resistance genes and further studying genes expression in Capsicum annuum L. seedlings under P.capsici stress.