Abstract: In order to evaluate the genetic diversity of cigar germplasm resources accurately, 92 cigars were analyzed with SSR primers. A total of 234 alleles were amplified and the average number was 5.441 9. The polymorphic information content of each locus varied from 0.099 5 to 0.846 9 with an average of 0.608 2. The average diversity index of Nei was 0.654 6, and the average of Shannon information index was 1.303 5. Unweighted pair-group method with arithmetic means cluster analysis showed that the tested cigar resources can be divided into 4 groups at the genetic distance of 0.35. The test materials were divided into 4 groups by principal component analysis and 5 groups by structure population genetic structure analysis. Although there were some differences in the groups divided by different analysis, the results were all related to the geographical origin. 15 core-primers were screened to construct the fingerprint database of the tested germplasms, which laid a theoretical foundation for the establishment on the identification system of cigar germplasm resources. This study provided scientific reference for cigar identification and evaluation, genetic background research, germplasm innovation and application.