Abstract：The genetic diversity of 51 parental lines used for hybrid production and breeding in Brassica napus L. was studied by SSR and SRAP markers, and the results of these two maker systems were compared. One hundred and ninety-four polymorphic fragments were detected using 45 SSR primer pairs, with an average number of polymorphic fragments per primer pair of 4.3. Whereas 197 polymorphic fragments were detected using 25 SRAP primer pairs, with an average number of polymorphic fragments per primer pair of 7.9. The 51 parental lines could be divided into five groups based on either SSR or SRAP markers by UPGMA cluster analysis. The main maintainer lines and restorer lines of Polima CMS were classified into the same group but different sub-groups. The groups classified by SRAP markers were more in accord with pedigree information than SSR markers.The SRAP markers were more effective in genetic analysis of closely related lines. The genetic distance calculated based on SRAP markers was larger than that on SSR markers. There is difference between the genetic diversity evaluated by SRAP and SSR markers, even though the same number of polymorphic fragments was used for evaluation. This difference may be caused by different numbers of variation alleles of the same gene detected by different primer sequences.
