Abstract:In order to understand the genetic diversity of Capsicum annuum germplasms, the coefficient of variation, diversity and principal components analysis of 34 phenotypic traits of 57 germplasms were studied, and the cluster analysis of them based on phenotypic traits and SSR markers were carried out, respectively. The results showed that there were significant differences in 34 phenotypic traits among Capsicum germplasms, the mean coefficient of variation and Shannon-Weiner diversity index were 40.67% and 1.20, respectively, and the 10 principal components could represent 75.972% of genetic information of phenotypic traits, the first principal component accounted for 22.317%, which was mainly composed of fruit transverse diameter, single fruit weight, shoulder shape and top character; the average Nei's genetic diversity index and Shannon information index of 19 SSR primers were 0.48 and 0.80, respectively. Based on phenotypic traits and SSR markers, fifty-seven Capsicum germplasms could be divided into 4 groups, but the correlation between two clusters was not significant (r=-0.175 9). So, these would provide theoretical basis for selection of parents and evaluation of germplasm resources in Capsicum breeding.