Objective  Genetic diversity and population structure of tea germplasms in Yongtai County were analyzed for resource utilization.

  Method  The EST-SNP molecular marker technology was applied to analyze the genetic relationships and diversity of 77 tea germplasms collected from Yongtai and surrounding areas.

  Result   Forty-eight SNP loci for identifying the germplasms were selected. The average polymorphism information index of the loci was 0.407 with an average observed heterozygosity of 0.303 and an expected one of 0.271, as well as the average fixed index of −0.092 and the frequency of secondary alleles of 0.268. The principal coordinate, cluster, and structure population structure analyses revealed that the interactions within a same population of the tea plants were stronger than among different populations at Yongtai, and that the tea germplasms found in Wutong significantly differed from those in Fukou, Danyun, and other places with significant genetic distance but close to those from Youxi and Datian. Using the 48 selected high-quality SNP loci, a library of the DNA fingerprints on 54 germplasms from Yongtai was established to provide a means for accurate germplasm identification.

  Conclusion   Yongtai County was rich in the resource of varieties of tea plants, which could be classified geographically into those from Wutong and those from Fukou, Danyun and other localities in the county. The cultivars from Wutong were more closely related to those found in Datian and Youxi, whereas those from Fukou, Danyun, etc. more to those existed in the north part of the county.