Abstract: To establish a systematic classification for the tea varieties in Fujian, Zhejiang and Guangdong, 20 pairs of SSR primers were selected in analyzing the genetic diversity and population structure of 64 tea cultivars commonly found in the regions. A total of 147 polymorphic loci were amplified with an average of 7.35 alleles per primer (ranging 3-15) and an average polymorphism information contentof 0.588 (ranged 0.267-0.851). The expected heterozygosity varied from 0.247 to 0.838 averaging 0.559; while, the observed heterozygosity, from 0.308 to 0.870 averaging 0.636. The Shannon index of the 64 teas was 1.271. The maximum ad hoc quantity, ΔK, was observed when K=4 in the population structure analysis, indicating that the entire collection could be divided into four subpopulations. Using a membership probability threshold of ≥ 0.50, 60 genotypes (accounting for 93.8% of the tested genotypes) were assigned to the four subpopulations, and 4(accounting for 6.2% of the tested breeding parents) retained in the admixed group.