Abstract: Owing to thinner hull, less fiber, higher oil and protein content than its black-seeded counterpart with a dark, thicker, and more lignified seed coat, yellow seeded variety is an important goal for breeding of oilseed Brassica napus. In order to investigate genetic classification and diversity, we tested the allelisms among different yellow-seeded accessions and studied the genetic diversity through clustering. Results showed that according to the result of allelism test, by investigation of the segregation of seed coat colour in F1 and F2 of cross between different accessions, 11 yellow-seeded rapeseed accessions could be divided into five groups: group Ⅰ including‘Youyan10’ , CZV55, E718, and Arm, mostly followed a dominant inheritance model; group Ⅱ including Q33 and D615, in incomplete dominant inheritance; group Ⅲ including 2006C, X2006, and 740C; the rest two groups only including Polo and HY15, respectively. The last three groups were generally in recessive genetic model. However, the inheritance of yellow- seeded traits of‘Youyan10’and 2006C was various from dominant to recessive when they crossed with the different genotypes of brownseeded. Cluster based on SSR molecular polymorphism showed that 35 yellow- seeded rapeseed accessions could be classified into three main groups: B.napus, B.rapa, and B.juncea. The group B.napus could be further divided into eight subgroups, the representations of them were 2006C and 740C, Youyan system, Q33, Ramiro from French, GQ4 from Shaanxi, Arm and prof from Canada, and yellow Polo from Polish cultivar Polo. This generally agrees with the pedigrees, breeders and originations. The results could provide the theoretical basis for the heterosis utilization of yellow- seeded rapeseed.