Abstract: To assess the genetic diversity and facilitate the management and identification of clones in the second-generation Cunninghamia lanceolata seed orchard, this study employed Simple Sequence Repeat (SSR) markers to analyze 119 clones from the second-generation seed orchard in Guangxi Provence,China. The results showed that 22 SSR primer pairs detected a total of 154 alleles. The mean number of alleles (Na) was 7, while the mean effective number of alleles (Ne) was 2.988. The average Shannon's information index (I) was 1.249. The mean observed heterozygosity (Ho) and expected heterozygosity (He) were 0.611 and 0.632, respectively, resulting in a mean fixation index (F) of 0.041. The average polymorphism information content (PIC) was 0.587, and the average null allele frequency was 0.030. Using the neighbor-joining method for cluster analysis,the 119 clones were divided into 5 groups.The average genetic differentiation coefficient of 0.046, the average genetic distance of 0.140 and an average gene flow of 4.318. 5% of the genetic variation originated from between populations, 2% from between individuals and 93% from within individuals.This indicates that the genetic differentiation coefficient and genetic distance between different groups were small, the gene flow was relatively high, and the genetic variation mainly existed within individuals,the genetic background was relatively homogeneous, and genetic differentiation was not significant. A subset of nine SSR primer pairs successfully distinguished all 119 clones. Based on these, a DNA fingerprint database was constructed, and unique QR codes were generated for each clone. This study provideed a reliable technical foundation for the precise identification of Cunninghamia lanceolata clones and supports future hybrid breeding programs.