Camellia sinensis var. assamica (Assam type), which served as special germplasm resource, were widely distributed and cultivated in geographical and ecological environments of the Yun-nan province. Due to redundant phenotypic variations, these materials become of importance in studies of tea evolution and breeding. The cultivar (cv.) Mengku-dayecha (MK tea) is a national sexual variety originated from Meng-ku town, Shuang-jiang County of Yun-nan province, and this genotype shows the characteristics of strong bud, leaf fertility and tenderness. MK tea becomes popular and is widely cultivated in the western and southern tea -producing counties of Yun-nan province. Within this study, 235 germplasm resources of MK tea plants, which were collected from Shuang-jiang county of Yun-nan province, were subjected to evaluate genetic diversity and genetic relationships among individuals, construct molecular fingerprints, select suitable core marker combinations, analyse population genetic structure. The results showed that: the polymorphism of each SSR marker had detected in the candidate samples. The alleles of markers ranged from 2 to 7 with mean value 3.84, and Ho ranged from 0.18 to 0.74 with mean value 0.47; the genotyping combinations by 25 SSR loci had confirmed to accurately identify each sample and each of them had been given a unique fingerprint. Indeed, 8 core SSR loci were successfully screened out as a simplified combination which had only 8.1 e-5 to 7.7 e-3 probability to appear the same genotype combination in the sample group; 235 samples collected from 11 regions were divided into 5 sub-populations (R, G, Y, Pi, Pu) and 3 groups (Pu + Y, R+G, Pi + Y) based on genetic structure analysis. Taken together, we proposed that R sub-population in ML and BD area was likely derived from the south area (NL), while group Pu + Y and group Pi + Y highly associated and originated from Y population. Notably, the genetic components of Pu and Pi populations assumed to be caused by the migration of tea resources in Dong-guo area.