In this study, 11 pairs of polymorphic SSR primers were employed to assess the genetic diversity, dissect the population structure, and construct DNA fingerprints for 205 clonal accessions of Schima superba. Across the 11 loci, a total of 184 alleles were detected, with an average of 16.7 alleles per locus (Na = 16.7). The mean values of effective number of alleles (Ne), Shannon’s information index (I), observed heterozygosity (Ho), and expected heterozygosity (He) were 8.158, 2.120, 0.694, and 0.793, respectively. The average polymorphism information content (PIC) was 0.776, with nine loci showing high polymorphism (PIC > 0.5). Fixation index (F) analysis revealed F > 0 at 10 loci, indicating an excess of homozygotes within the population. UPGMA clustering based on genetic distances divided the seven geographic populations into two major groups, with the Ziyuan (ZY) population exhibiting significantly larger genetic distances from the other six populations (0.377 - 0.526) than the average distance within the latter group (mean 0.192). Population structure analysis (K = 4) and principal coordinate analysis (PCoA) also supported the subdivision into four subgroups, but with substantial overlap among subgroups, reflecting frequent gene flow. Among the six nonZY populations, Fst values ranged from 0.013 to 0.045, whereas Fst between ZY and the others ranged from 0.088 to 0.123, with corresponding gene flow (Nm) estimates of 5.350 - 19.721 and 1.784 - 2.589, respectively. AMOVA showed that variation among populations accounted for only 4%, among individuals within populations for 10%, and within individuals for 86%, indicating that genetic variation was predominantly distributed within individuals. A DNA fingerprinting profile for the 205 accessions was successfully constructed using binary “0/1” coding. Collectively, the clonal germplasm of Schima superba harbors abundant genetic diversity with weak interpopulation differentiation, and intraindividual variation is the primary source of total variation. The ZY population displays pronounced genetic uniqueness and merits prioritized conservation and utilization. The established fingerprinting system can facilitate germplasm identification, core collection construction, and parental selection in breeding programs.