The primary goal of this research was to learn the genetic diversity among the common and released tea varieties in Taiwan. Samples of 48 cultivars for the research were collected from the germplasm nursery of Taiwan Tea Experiment Station (TTES). The AFLP and RAPD molecular marker systems were applied to the analysis of the genetic diversity of the samples. Eight primer combinations of the AFLP primers were used in the analysis and resulted in more than six hundred bands. Four hundred and twenty three polymorphic bands were identified. The estimated genetic distance among the samples were ranging from 0.02 to 0.97. The samples were divided into three groups based on the cluster analysis of the estimated distance with UPGMA methodology. The number of varieties in each one of the three groups was 33, 12, and 3, respectively. Thirty-seven genotypic specific bands belong to 15 varieties were identified in the AFLP analysis. Twenty-four informative random primers selected from the survey of 100 primers were used to dissect the genetic diversity of the same set of samples. More than two hundred DNA fragments were amplified by the primers and 103 fragments were identified as polymorphic. The estimated genetic distance among the samples with the RAPD polymorphic fragment were ranging from 0.03 to 0.96. The samples were also divided into three groups based on the cluster analysis of the estimated genetic distance with UPGMA methodology. The grouping between the results of AFLP and RAPD analysis was showed to be less than 10% of discrepancy. The relationship between the samples revealed by the DNA markers was also consistent with the pedigree records. The genetic diversity between the 18 released cultivars was suspected to be convergent in the literatures was proven to be otherwise with the evidence from the results.