The invention belongs to the biotechnology field, provides an obtaining method of molecular markers related to chrysanthemum drought resistance, and is used for positioning and cloning of a chrysanthemum drought resistance excellent gene and breeding of new chrysanthemum varieties. The obtaining method comprises the steps: a, identification of the drought resistance; b, analysis of a chrysanthemum variety group structure; c, analysis of chrysanthemum variety genetic relationship; and d, determination of the molecular markers closely related to the chrysanthemum drought resistance. The method simultaneously adopts three molecular marker techniques comprising SRAP, SCoT and EST-SSR, the principles are different with each other and each have pertinency, and obtained dyeing strips are good in polymorphism and high in repeatability, can cover the entire genome, have rich number of strips and are beneficial for obtaining the molecular markers closely related to the drought resistance. 8 molecular markers related to the chrysanthemum drought resistance are totally obtained, early selection, directional selection and accurate selection of excellent drought-resistant varieties are achieved, the work load can be reduced, and the selection efficiency of chrysanthemum drought resistant genotypes is greatly improved, so as to speed up the process of breeding.