A restriction fragment length polymorphism (RFLP) marker, HC352b, has identified as closely linked to the CRa locus responsible for clubroot resistance (CR) in a study dissecting CR loci in Chinese cabbage (Brassica rapa L. ssp pekinensis). Unfortunately, the RFLP pattern, including HC352b detected by the cDNA clone HC352, was complicated and confused in its interpretation because it represented multiple-copy loci. To provide a practical HC352b marker for CR breeding programs, a sequence characterized amplified region (SCAR) marker was constructed along the analysis of HC352 genes, followed by its evaluation for CR selection. Schematic characterization of signals was achieved by identification of HC352 homologous genes with their restriction sites, employing CRa-positive and -negative doubled haploid (DH) lines. Genomic sequence information from a set of HC352 homologous genes was analyzed to identify the CRa linked paralog HC352b, followed by the successful designation of a SCAR marker. This correctly predicted the CR phenotypes of all tested individuals of F 2 and back-crossed progenies.