Pepper is an important plant worldwide for its economic benefits and nutrition values. Pepper bacterial wilt (PBW) is one of the most destructive diseases, when plant is diagnosed bacterial wilt, it could be observed browning stem, wilting leaves and lethal characteristic. Ralstonia solanacearum is a gram-negative pathogen which cause bacterial wilt in many plant species. It could infect host by getting into root, block the vessel of xylem, eventually obstruct water sent to the top of the plant and cause death. PBW is difficult to control in the field, resistance source selection has been regarded as one of the most effective methods to prevent it. Cotyledon seedling screening method is a rapid way to screen resistant materials against PBW during the cotyledon seedling stage. The objective of this research is assessment of the pepper germplasm resistance to bacterial wilt using cotyledon seedling screening method and identify candidate loci that regulate the resistance. In this research, we analyzed the association between the phenotypes and the genotypes of the pepper collection, and significant SNPs have been found. Whether the significant loci can regulate the resistance of Capsicum species will require further investigation.