Two tea cultivars, Tieguanyin and Huangdan, are used as main parents in oolong tea breeding. Fuding Dabaicha is considered as one of core parents in breeding of green and black tea plants. So far, Many quality tea cultivars have been bred based on these cultivars. Therefore, research on the genetic diversity and fingerprint map of these parents and their superior derived varieties are considerably important, which can contribute to the selection of breeding materials and the protection of plant variety right. In this study, the genetic diversity and relationship of 13 Oolong tea varieties and 21 green tea varieties were analyzed by 40 SSR markers. The average genetic diversity (H) and genetic distance of 34 samples were 0.54 and 0.58, respectively, which means that the genetic diversity of the accessions tested were relatively high with rich variation. Furthermore, 90% genetic diversity came from genetic differences of tested materials. These samples were divided into two groups according to its breeding source using UPGMA method. Moreover, the genetic structure of two sets of varieties is different. In consideration of good stability and high polymorphism, 5 out of 40 pairs of SSR primers were selected and combined to construct the fingerprinting maps of 34 materials.