Abstract: Female parent purity is crucial for affecting hybrid seed purity in Brassica napus hybrid seeds production. To investigate an effective method suitable to the identification of the false hybrid sample with genotype of female parents in hybrids samples, this paper adopted CTAB method to extract the total DNA of hybrid F1 seedlings and its seed coats respectively. Then, the DNA was used to screen the SSR primers which could distinguish the hybrid seeds from female parents, and the primers obtained were used to identify the false hybrid sample with genotype of female parents in hybrids samples. The results showed that hybrid F1 seedlings and its seed coats had the same SSR fingerprinting, and the coincidence rate was over 98% between the SSR detection results obtained by the method in this study and field performance, this results indicated that the method for detecting the false hybrid sample with genotype of female parents in hybrids samples was reliable. The method of this research can overcome the dependence of current SSR identification rapeseed hybrids purity on its parents, provide technical reference on seed production and seed purity quality control management of business departments.