SCoT-PCR amplification system is constructed to analyze the tea resources in Fujian. Totally 16 polymorphic primers were screened from 38 SCoT primers to construct fingerprints of 55 tea cultivars (lines). A total of 219 bands were amplified from 55 materials, with 216 polymorphic bands. The average bands amplified by each primer and polymorphic ratio were 13.8 and 93.15%. The Genetic similarity (GS) of 55 tea resources ranged from 0.49 to 0.85, with an average of 0.67. The SCoT marker analysis showed that the observed number of alleles was 1.93 in these two tea groups. The effective number of alleles, Nei gene diversity, Shannon’s information index, genetic differentiation and the gene flow were 1.54, 0.32, 0.48, 0.067 and 7.01, respectively. When the genetic similarity coefficient was set to 0.64, the tea resources could be divided into two major categories.