Abstract: The paper aims to study the genetic diversity of tea germplasm in Baiying mountain. The capillary electrophoresis detection with fluorescent EST-SSR marker was used to analyze the genetic polymorphism and genetic relationship of 68 tea plant germplasm. The results showed that: (1) the population biology morphological variation was very rich, covering trees, small trees and shrubs; large leaf, middle leaf and small leaf; oval, oblong and lanceolate; the amount of bud fuzz changed continuously from less to more; (2) the 34 pairs of EST-SSR primers showed that the average of heterozygosity was 0.6981 in Baiying mountain, the observe heterozygosity was 0.5982, the polymorphism information content was 0.6686, the Shannon’s information index was 1.6068; the number of digits and observed alleles were 4.1761 and 9.7353, respectively; (3) the tea germplasm was divided into 5 subpopulations based on Evanno statistical model, the gene flow value among five subpopulations was 1.8995, and the coefficient of genetic differentiation between populations (Fst) was 0.1163. Each subgroup was a moderately differentiated group. There were gene exchanges among subgroups.