In this paper, we selected 7 rapeseed germplasms with super-high oil content and 16 main rapeseed cultivars from the different planted regions to construct their fingerprinting by SSR molecular markers. Using 28 SSR primer pairs from the different linkage groups, we totally got 302 SSR bands for the all materials, 279 of which are polymorphism bands, each primer amplified 6-16 bands with 10.79 bands on average, the average of polymorphism rate reach 92.38%. By this way, we could distinguish all the materials better. UPGAM analyzing revealed that there were the large difference among the high oil content germplasms and between the high oil content germplasms and the main cultivars. At genetic distance of 0.171, the 23 B. napus could be divided into nine groups, in which the super- high oil content germplasms were divided into four groups, and 8 main cultivars were divided into five groups. These results showed that all materials had the most abundant genetic diversity, especially there were large genetic differences between the super-high oil germplasms and the main rapeseed cultivars.