A core set of SSR markers which represent the maximize watermelon genetic diversity was used to analyze the genetic diversity of 24 example varieties in watermelon DUS testing, then the SSR fingerprint database of these varieties was constructed. Based on the SNP-based dendrogram for the 17 resequencing lines, we evaluated the genetic relationship among these varieties, and they were classified into 3 groups with the similarity coefficient of 0.80, this marker-based clustering showed more accurate than the traditional morphological clustering. Using two-dimensional (QR) code, the SSR fingerprint database of 24 example varieties was constructed. The utility of this detection system in DUS molecular test was analyzed using a PVP varieties "Jingxin No. 2" and its control "Jingxin No. 1", there were 4 polymorphic alleles among 32 alleles and their similarity coefficient was 0.89. It showed more polymorphic alleles and more accurate than morphological identification. The SSR fingerprint database of example varieties and molecular detection system used in this study can be applied in DUS molecular test of watermelon. Moreover, they will provide a basis for genetic purity, genetic background screening and authenticity fast evaluation of watermelon.