Heterosis plays an essential role in breeding system to develop new characters in many crop plants. In rapeseed, there are several approaches for utilizing heterosis in breeding,  such as genic male sterility  (GMS), cytoplasmic male sterility (CMS), transgenic male sterility (TMS), self-incompatibility (SI) and chemical hybridizing agents (CHA). Of these, some CMS systems such as Pol CMS and Ogu CMS have been widely used for production of commercial rapeseed. Pol CMS line has maternally transmitted trait resulting in the failure of self-pollination, while nuclear genes, fertility restorers (Rf) have the function to suppress the male-sterile phenotype. The pol CMS from the cultivar ‘Polima’ confers complete male sterility to many B. napus cultivars. To develop new markers related in pol CMS, we analyzed B. napus cultivars including male fertile and sterile groups using a genome-wide association study (GWAS) and classified 4 groups by restoration phenotypes of each F1 male sterility. From bulk segregant analysis (BSA), we isolated several thousands of new SNPs (Single Nucleotide Polymorphisms) between male fertile and sterile cultivars and developed a new CAPS (Cleaved Amplified Polymorphic Sequence) marker strongly linked to the Polima male sterility. Also we found new candidate genes linked to Ogu CMS based on SNP difference using Ogu CMS population. The objectives of this study is to develop additional molecular markers and candidate genes linked to the Rfp and Rfo genes in B. napus and other Brassica species. This information will help to determine the Rfp and Rfo genotype in heterosis breeding system and to achieve map-based cloning of these gene.