120 pairs of SSR primers and 63 pairs of InDel primers were used to determine genetic variation among diploid, triploid and tetraploid watermelon genomes. The results showed that 113 pairs of SSR primers and 63 pairs of InDel primers could be successfully amplified. There was slight difference between diploid and tetraploid watermelon genomes in the aspect of SSR. Among 120 pairs of SSR primers, 2 showed obvious polymorphism with polymorphic rate of 1.67%, corresponding to 34047313-34063581 intervals on chromosome 9. 1 gene encoding zinc finger protein was predicted in polymorphic interval which could regulate the expression of other genes at the level of transcription and translation. There was no significant difference in the aspect of InDel among watermelon genomes with different ploidy which indicated that the genomic insertion and deletion site was not changed before and after chromosome doubling. The results indicated that watermelon genomic structure had no significant change in the process of polyploidization. The difference of traits between tetraploidy and diploid parent might be closely related with epigenetic regulation. This study could provide scientific basis for ploidy breeding, new variety improvement and germplasm innovation.