Amplified fragment length polymorphism (AFLP) analyses were used to assess genetic diversity among 30 genotypes of watermelon [Citrullus lanatus (Thunb.) Mansf.] representing a broad genetic base, including breeding lines and commercial germplasm. Eight AFLP primer combinations selected from 64 primer combinations were polymophic. The polymorphism was 13.0% to 31.9% within the 28 cultivars examined, and 45.3% to 64.2% among all the genotypes. Each genotype could be successfully distinguished based on AFLP scoring. Cluster grouping of accessions based on the AFLP analysis was consistent with that from classification by pedigrees and ecotypes.