EST-SSR molecular markers were used to identify the hybrids of two F1 crosses, which was derived from the variety ‘Fuding Dabaicha’ and ‘Anhui 1’ as the female parent and ‘Baojing Huangjincha 1’ as the male parent, followed by a genetic diversity. The results showed that 41 (85.42%) of 48 progenies from Fuding Dabaicha were identified to be true F1 hybrids, while among 35 strains (79.55%) of 44 plants from Anhui 1 were true hybrids. Genetic analysis using 17 pairs of SSR primers revealed 41 alleles in the two hybrid populations with an average of 2.82 (Fuding Dabaicha) and 2.71 (Anhui 1). No significant difference on the genetic diversity parameters of the two hybrid F1 populations were detected. The mean values of Nei, He, Ho, I were 0.56, 0.78, 0.43, 0.93 (Fuding Dabaicha) and 0.55, 0.75, 0.43, 0.90 (Anhui 1), respectively. The variation range of genetic similarity coefficient in F1 hybrid of Fuding Dabaicha × Baojing Huangjincha 1 and Anhui 1 × Baojing Huangjincha 1 was between 0.44~0.90 and 0.48~0.95 respectively. The cluster analysis using UPGMA showed that two hybrid populations were divided into three groups when the similarity coefficient was 0.60 and 0.64 respectively. The progenies were clustered together and represented a higher genetic similarity with respective female parents than the male parent. Collectively, this study reported an example on the genetic classification of tea hybrids using EST-SSR markers.