Abstract: 【Objective】Molecular fingerprinting and genetic diversity analysis are important for protecting and managing superior germplasm resources, as well as for identifying superior clones. 【Method】In the present study, 11 SSR primer pairs were used to assess the genetic diversity and DNA fingerprints of 89 C. fortunei clones. 【Result】A total of 53 putative alleles were detected from 11 pairs of primers, with a mean of five putative alleles per locus, ranging from three to six. The number of effective alleles(N_e)ranged from 1.887 0 to 4.295 6, with a mean of 3.041 1, and the Shannon's information index ranged from 0.774 9 to 1.556 3, with a mean of 1.208 1. These findings indicate that SSR markers in C. fortunei exist a relative high polymorphism. Furthermore, according to the characteristics of the SSR markers and primer sequences, the present(recorded as 1)and absent(recorded as 0)collected from amplification by SSR markers were transferred into genetic types. By combining different genetic types code, we established DNA fingerprints of 89 C. fortunei clones, and attached a 22-digit fingerprint number to each clone. The 89 clones were also separated into five clusters based on genetic distance. 【Conclusion】SSR markers are suitable for analyzing and identifying the genetic diversity of C. fortune, and C. fortune shows moderate to high genetic diversity.