Watermelons are genetically modified in the sense that selective breeding is used to grow them. These days a vast majority of food crops have been altered genetically in some way by the people who grow them.
Most of the crops today are modified not through gene splicing, but rather over time through thousands of years of carefully selecting certain crops to cross breed with one another.
Seedless watermelons for example are the result of selective breeding as well as hybridization which is technically not genetic manipulation in the traditional sense. These seedless watermelons have been around a lot longer than genetic food manipulation and have gotten to where they are over thousands of years.