Abstract:To explore the genetic diversity of cultivated ancient tea tree (Camellia sinensis var. assamica) germplasm resources, the genetic diversity and structure of 64 germplasm resources in the ancient tea garden of Wuliangshan Town, Nanjian County were analyzed by using EST-SSR molecular markers. The results showed that a total of 223 alleles were detected with 20 pairs of primers, and the average effective number of alleles among populations was 3.48. The average observed allele (Na), average effective allele (Ne), average Shannon diversity index (I), and average of Nei’s gene diversity index (H) were 6.25, 2.983, 1.251 and 0.646, respectively. POPGENE analysis showed that the mean genetic differentiation coefficient (Fst) was 0.063, indicating that there was moderate differentiation among populations with gene flow (Nm) of 3.710. AMOVA molecular variance analysis showed that 14% of genetic variation in C. sinensis var. assamica occurred among populations and 86% occurred within population, indicating that genetic variation in C. sinensis var. assamica mainly occurred within population and genetic exchange was abundant. The rich genetic diversity of the ancient tea tree population in the ancient tea garden of Nanjian County would provide a scientific basis for the protection and utilization of C. sinensis var. assamica germplasm resources and the selection of new varieties.