Abstract: 【Objective】 In this study, the genetic diversity of 41 yellow pepper germplasms resources was analyzed, the germplasm resources of yellow pepper with good resistance and good quality were screened for yellow pepper variety breeding in Fujian.【Method】 Based on 41 accessions of yellow pepper germplasm resources, 12 quantitative traits and 10 descriptive traits were observed and analyzed, and genetic diversity was analyzed by amplification of SRAP molecular markers. Based on phenotypic data and SRAP molecular marker amplification, cluster analysis was performed.【Result】 The coefficient of variation of 12 quantitative characters ranged from 14.20% to 39.98%, with an average of 26.61%. The coefficient of variation of petiole length, fruit length, single fruit weight and fruit number per plant were all greater than 25.00%, indicating that there were abundant variations in these traits and had a good basis for genetic improvement. The diversity index of 10 descriptive characters ranged from 0.1985 to 1.0791, with an average of 0.5061. The anthocyanin color rendering degree was high, and the diversity indexes of internode hair, growth vigor and plant morphology were low. Based on phenotypic clustering analysis, the 41 yellow pepper germplasm resources could be divided into four classes, Ⅰ group included 11 yellow pepper germplasm resources, Ⅱ group included 14 yellow pepper germplasm resources, Ⅲ group included 5 yellow pepper germplasm resources, Ⅳ group included 13 germplasm resources. The 41 yellow pepper germplasm resources with similar traits clustered into a group. In SRAP analysis, a total of 117 bands were detected by 14 primer pairs, among which 90 bands were polymorphic, and the polymorphism ratio was 76.92%. Cluster analysis results based on SRAP molecular markers showed that similarity coefficient between material was 0.80-1.00, the genetic similarity coefficient was at 0.85, yellow pepper materials were divided into 6 groups, the Ⅰ and Ⅵ groups only contained one sample material, the group Ⅱ included 4 samples, Ⅲ group included 29 samples material, and Ⅳ and Ⅴ groups included 3 samples material, materials from the same were in the same cluster. It could be seen that the clustering results based on SRAP molecular markers were more inclined to the distance of kinship than the clustering results based on phenotype. 【Conclusion】 The germplasm resources of yellow pepper have rich genetic diversity. Using SRAP molecular markers to assist the breeding of new varieties of yellow pepper, screen out the homozygous materials with excellent comprehensive traits and distant genetic relationship, which can effectively solve the problems of low parental selection efficiency and slow breeding process in pepper breeding