Clubroot caused by Plasmodiophora brassicae is a devastating disease of Cruciferous crops. Developing cultivars with clubroot resistance (CR) is the most effective control measure. For the two major Brassica vegetable species B. rapa and B. oleracea, several commercial cultivars with unclear CR pedigrees have been intensively used as CR donors in breeding. However, the continuous occurrence of CR-breaking makes the CR pedigree underlying these cultivars one of the breeders' most urgent concerns. The complex intraspecific diversity of these two major Brassica vegetables has also limited the applicability of CR markers in different breeding programs. Here we first traced the pedigree underlying two kinds of CR that have been widely applied in breeding by linkage and introgression analyses based on public resequencing data. In B. rapa, a major locus CRzi8 underlying the CR of the commercial CR donor ‘DegaoCR117’ was identified. CRzi8 was further shown to have been introgressed from turnip (B. rapa ssp. rapifera) and that it carried a potential functional allele of Crr1a. The turnip introgression carried CRb, sharing the same coding sequence with the CRb that was also identified from chromosome C07 of B. oleracea CR cultivars with different morphotypes. Within natural populations, variation analysis of linkage intervals of CRzi8, PbBa8.1, CRb, and CRb yielded easily resolved InDel markers (> 20 bp) for these fundamental CR genes. The specificity of these markers was tested in diverse cultivars panels, and each exhibited high reliability in breeding. Our research demonstrates the value of the practice of applying resequencing big data to solve urgent concerns in breeding programs.