Abstract: In order to promote the development and utilization of cigar tobacco germplasm resources in Sichuan, genetic diversities of 20 cigar tobacco germplasm resources were analyzed based on agronomic traits and SSR markers. The results showed that the germplasm had rich genetic diversity, the coefficients of variation of agronomic traits ranged from 6.59% to 19.97%, and the genetic diversity indexes were from 1.69 to 2.18. The germplasm were grouped into four categories, and the agronomic traits differed significantly among the categories. According to the principal component analysis and genetic structural analysis based on SSR markers, the tested germplasm were divided into three groups. The tested germplasm could also be clustered into four groups according to the cluster analysis, which provided clues for the source trace of cv. Dexue 1, Dexue 2, Dexue 3 and Shiyanyihao.