Genomic DNA of watermelon was analyzed by optimizing the concentration of Mg~(2+), dNTPs, and primer in RAPD and ISSR analysis systems. The screened optimization system of RAPD for watermelon genomic DNA was 20 μl, which contained primer 0. 4 μmol/L, dNTPs 200 μmol/L, Mg~(2+) 2. 0 mmol/L, DNA 20 ng, 1 ×Buffer, Taq E 1. 0 U.The optimization system of ISSR was 16 μi, which contained primer 0.25 μmol/L, dNTPs 160 μmol/L, Mg~(2+) 1. 0 mmol/L,DNA 20 ng, 1×Buffer, Taq E 0. 64 U. RAPD and ISSR were applied in polymorphism analyses of watermelon mapping parents, 64-1⊕-3 and 6⊕-2, and 23 ⊕-1 and 4-1 ⊕-2, which were self lines of district variety far from zoology. The results of mapping parents 64-1⊕-3 and 6⊕-2 showed that 170 out of 181 RAPD primers generated 525 amplified bands with an average of 3. 08 gene loci per primer, and of the 170 amplified primers, 55 could test the polymorphic loci, which produced 77 polymorphic bands, and the polymorphism rate was 14. 67%; 45 out of 62 ISSR primers generated 188 amplified bands with an average of 4. 18 bands per primer. And 15 polymorphic primers produced 23 polymorphic loci in mapping parents 64-1⊕-3 and 6⊕-2. One polymorphic primer could amplify 1. 53 polymorphic loci averagely. The polymorphism rate of ISSR analyses was 12. 23%. In mapping parents 23⊕-land 4-1⊕-2, 456 out of 499 RAPD primers amplified 1431 bands with an average of 3. 14 bands per primer, and 142 polymorphic primers produced 240 polymorphic loci, and the polymorphism rate was 16. 77%. These showed that the genetic background of watermelon mapping parents was narrow.