Abstract: Molecular marker technique of SCoT was applied to analyze the genetic diversity of the sugarcane varieties (or lines) bred at Fujian Academy of Agricultural Sciences, along with the conventional cultivars for comparison. Establishment of the genetic relationship among the germplasms provided the needed reference for breeding and identification of the existing resource. Fifteen SCoT primers were selected to amplify the genome DNAs of 23 test materials. A total of 122 loci, with 56.56% of them polymorphic, were obtained averaging 8.1 bands detected by each primer. A clustering analysis revealed a minute genetic difference existed among 23 sugarcane varieties with a similarity coefficient ranging from 0.77 to 0.98, indicating a close relationship in origins of the breeding parents, duplicated applications, and low genetic diversities among the cultivars.