The genetic diversity of watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] in China, the world's largest producer of watermelon fruits, has not been examined. Two molecular markers, sequence-related amplified polymorphism (SRAP) and simple sequence repeat (SSR), were used to investigate the genetic variation and genetic relationship among 54 Chinese watermelon accessions, as well as 7 accessions from Africa, the United States, and Japan. SRAP assay generated 312 bands, of which 163 were polymorphic, while SSR assay detected 101 alleles with 87 polymorphic alleles and 114 genotypes. A comparative analysis of the diversity index, effective multiplex ratio, and marker index of the 2 markers showed higher efficiency of SRAP markers in watermelon germplasm fingerprinting. The Mantel test resulted in a high correlation between SRAP and SSR data with a value of γ = 0.863, revealing a good fit between the 2 marker systems. Genetic diversity among the accession set was estimated by a construction of dendrograms using SRAP, SSR, or SRAP-SSR combined data. There was clear consistency between the 3 dendrograms on the positioning of most accessions. The study demonstrated that most Chinese cultivated germplasms (CCGs) were clustered independently of their geographical distribution and horticultural classification, and had a narrow genetic base; most CCGs and foreign cultivars had a high genetic closeness and showed similar lineages; and the 4 wild accessions were the most genetically diverse, followed by the small-fruited accessions from northern China and edible-seeded accessions. We concluded that CCGs lacked genetic variation, and we offer a means of introducing new genetic diversity into the watermelon germplasm pool in China, which is essential to maximizing productivity in watermelon.