Abstract: There were many PCR-based molecular marker techniques, but their own disadvantages limited the development and application. A new molecular marker system-SRAP (Sequence-Related Amplified Polymorphism) showed the good development future by its unique virtue. It was used mainly in foreign countries and seldom in domestic country. The factors of reaction system were modified in order to simplify processes and better system with watermelon. The principle, characters and application of SRAP also were introduced. The result showed good effect. SRAP will be a valuable tool in research area.