Objective  Genetic diversity and structure of the tea germplasms in Yunxiao were studied to facilitate the collection and utilization of the natural resource.

  Method   SNP molecular marker was used to analyze the genetic relationship and diversity of 61 varieties of Camellia sinensis in Yunxiao, Fujian.

  Result  The mean polymorphism information index, observed and expected heterozygosity, fixed index, and minor allele frequency of the SNP marker were determined to be 0.415, 0.309, 0.260, −0.072, and 0.197, respectively. Sixty-six high quality loci that could effectively and accurately identify the genetic relationship of tea plants were obtained. The genetic distance of 6 populations ranged from 0.150 to 0.926. The DNA fingerprints of the germplasms were constructed. The principal coordinates analyses and cluster analyses showed the component distribution to be relatively close within a population and the exchanges among the groups evident. Of the varieties, Xiaomaoshan was the richest in genetic diversity.

  Conclusion  The genetic diversity of tea germplasms in Yunxiao was vast with populations of high geographic differentiation and in-between group exchanges. The SNP molecular marker-based technology was proven applicable for identifying the germplasms benefitting the utilization of local tea resource for selection and breeding.