To select suit parents was the key work of hybridization in Brassica napus L. The genetic diversity of 180 parental germplasm of yellow-seeded B. napus provided by the Chongqing Rapeseed Engineering Research Center of Southwest University were analyzed. 308 alleles were detected via 60 SSR primer pairs which were selected from the different linked groups in Brasicca napus, , among them 207 polymorphic bands were obtained, accounting for 67.2% of the total bands. The UPGMA cluster analysis based on SSR data showed that 180 parental lines could be classified into three groups at the threshold 0.566 of genetic distance, which agrees with the pedigree analysis. 20 samples were chosen as core collection by the pedigree, genetic distance and five quality traits of germplasm characteristics. The results showed that the SSR markers could be explained the genetic diversity B. napus accessions appropriately. It was an effective method to develop a core collection of the crop by SSR markers and germplasm characteristics. It could also provide the theoretical basis for the hybridization and breeding of yellow-seeded Brassica napus.