Ralstonia solanacearum causes one of the most common soil-borne vascular diseases of diverse plant species, including many solanaceous crops such as tomato and pepper. The resulting disease, bacterial wilt (BW), is devastating and difficult to control using conventional approaches. The aim of this study was to investigate the differentially expressed genes in pepper root systems in response to infection by R. solanacearum. DNA microarray (Capsicum annuum 135K Microarray v3.0 Gene Expression platform) analyses were performed using a susceptible genotype, Chilbok, and a resistant genotype, KC350, at 3 time points (1, 3, and 6 days post inoculation). We identified 115 resistance-specific genes (R-response genes) and 109 susceptibility-specific genes (S-response gene), which were up-regulated in 1 genotype, but down-regulated in the other genotype. Gene Ontology (GO) analysis for functional categorization indicated that many R-response genes were related to genes that function in xyloglucan biosynthesis and cell wall organization, while S-response genes were involved in the response to stress and cell death. The expression of genes encoding xyloglucan endotransglycosylase/hydrolase (XTH) and b-galactosidase were verified by real-time RT-PCR at an early time point of R. solanacearum infection. The results supported the idea that rapidly induced XTH expression in KC350 may play an important role in the restructuring and reinforcement of the cell wall and restrict bacterial movement in xylem vessels. In addition, induced expression of b-galactosidase in R. solanacearum-infected Chilbok implied that degradation of the cell wall structure in vascular tissues by b-galactosidase might be an important factor facilitating R. solanacearum invasion of and movement in susceptible host plants.