To elucidate the differential gene expression patterns in soybeans during infection by Phytophthora sojae, a cDNA libraryfor suppression subtractive hybridization (SSH) was constructed with cDNAs from soybean cultivar Suinong 10 treatedwith sterile distilled water as the driver and cDNAs from Suinong 10 inoculated with P. sojae as the tester. A total of 2 067recombinant colonies from the SSH library were randomly picked, amplified, and sequenced. After discarding 312 poorquality expressed sequence tags (EST), 1 755 high quality ESTs were assembled and edited to 1 384 tentatively uniquegenes (TUG), in which, 586 showed significant homology to known sequences, and 798 had low homology or no matchwith the known sequences. A cDNA microarray containing 307 singletons from the 586 TUGs and 222 singletons from the798 TUGs was developed to characterize differentially expressed cDNAs in the SSH library, and eight cDNAs wereidentified to be up-regulated after microarray analysis and then confirmed by real-time PCR. They were homologous to theprotein 10, and were also related to some proteins in disease resistance response, such as pathogen-related protein,phenylalanine ammonia-lyase, isoflavone reductase, WRKY transcription factor 31, major allergen Pru ar 1, and pleiotropicdrug resistance protein 12. Most of the up-regulated cDNAs encode enzymes of phytoalexin biosynthesis andpathogenesis-related proteins involved in plant disease resistance. Here, we fist reported the Pru ar 1 in soybeans. Thefindings of this research have contributed to better understanding of soybean resistance to P. sojae at the molecular level.