Guizhou has the largest tea planting area in China, which also has the abundant tea plant germplasm resources. Accurate identification of the authenticity and genetic structure of the cultivars is the pivotal to germplasms identification and parents selection in hybridized breeding. In this study, 54 tea plant germplasms including the cultivars or improved cultivars in Guizhou province were used as materials, the genetic identification of them was conducted using 35 SSR markers, firstly. A total of 317 alleles were detected, yielding the polymorphic information content (PIC) ranged from 0.22 to 0.92, with a mean value of 0.73. The genetic differentiation of each SSR marker was evaluated by PI and PIsibs, which showed that any two pairs of primers could distinguish the tea plant germplasms in this study. Five core SSR markers were selected to generate the fingerprinting of these tea plant resources, which provided the resolution sufficient for identification of the individuals in larger groups. Additionally, by using the genotyping-by-sequencing (GBS) approach, the genome-wide SNPs were identified with the 54 cultivars or improved cultivars, and a total of 698117 high quality SNPs were identified. The phylogenetic analysis, principle component analysis (PCA) and genetic structure analysis of the 54 tea plant samples were performed. The 54 tea plant germplasms were divided into 4 sub-populations, and the genetic backgrounds of the cultivars and the improved cultivars were highly overlapped. According to the results, the general breeding model of tea plants in Guizhou in the previous was speculated, which revealed that the germplasms utilization of early tea plants breeding in Guizhou depended too much on Fudingdabaicha and the local tea plant germplasm resources of Yunnan province, and it was also shown that increasing the hybrid utilization of the excellent tea plant cultivars in other provinces and the ancient tea plant resources in Guizhou would contribute to the germplasm innovation and the breeding of new tea plants in the subsequent breeding practice.