Abstract: To identify and select tea germplasms in Yunxiao andYouxi counties in the wild, genetic diversity and relationship of the collectedsamples were analyzed in reference to the major cultivated tea varieties in theprovince by the technique of capillary electrophoresis using EST-SSR markers.The wild-type specimens were genetically remotely related to the referencevarieties. The Yunxiao germplasm was somewhat close to Phoenix Narcissus andothers from Guangdong province, whereas the Youxi samples differed greatly fromthe reference. The mean allele number, effective allele number, expectedheterozygosity, and Shannon diversity index of the Yunxiao germplasm were3.896, 2.455, 0.5264, and 0.9463, respectively, while those for the Youxispecimen, 3.310, 2.290, 0.4980, and 0.8595, respectively, indicating arelatively rich diversity. The Nei’s genetic distance, genetic differentiation index, andmolecular variance analysis (AMOVA) on the populations exhibited a significant21% variation. The results provided a basis for further exploitation,utilization, protection, and breeding of tea resources in the wild in Fujian.