Soybean cyst nematode (Heterodera glycines, SCN) is one of the important pests on soybean (Glycinc max).Resistance cultivar is most effective and environmentally benign method to control SCN.In China, we have found large amount of resistance germplasm resources from the background of Chinese small black soybean (called Xiaoheidou) to SCN.However, the resistance mechanism was not very clear in most cultivars.This job utilized Huipizhi Heidou as the incompatible line in contrast to Liaodou15 as the susceptible line in Liaoning province.Sequencing the soybean root cDNA library after infected SCN J2 10 days and analyzing the differential gene expression under Solexa the high-throughput sequencing technique, there were 389 genes up-regulated and 344 genes down-regulated.Therefore, as the control, Liaodou15 the susceptible line showed the 222 genes up-regulated and 691 genes down-regulated.The gene functional analysis revealed the differential expression genes distribute the metabolism pathway involved in sugar, lipid, amino acid, energy and secondary metabolism.Further, Gene ontology (Go) enrichment of differential genes and DGE analysis of Huipizhi black soybean were examined in Plant-pathogen interaction, α-linoleic acid metabolism and phenlypropanoid biosynthesis metabolism may play an important role in suppressing SCN.The analysis of differential expressed genes between the incompatible line and compatible line showed that the chitinase I, amino acid transporter and metallothionein were broad spectrum resistance related genes.Moreover, the 77 genes were up-regulated in resistance line and down-regulated in susceptible line, LRR receptor kinase, transcription factor WRKY family and CDPK were the members of plant defense system, and involved in the defense response to suppress the pathogen.