Clubroot is an important disease of cruciferous crops caused by Plasmodiophora brassicae, and pathotypes are classified based on the response of differential hosts. This study was conducted to identify genetic markers able to differentiate pathotypes. Differential expression of genes between pathotype 4 (P4) and pathotype 7 (P7) was assessed according to transcriptome data of molecular marker screening. Among the pathotypes (P2, P4, P5, P7, P9, P10, and P11) tested, six genes were exclusive to P4, dividing the isolates into three types: PBRA_003263 and PBRA_003268 were present in all P4 isolates, PBRA_000003/Novel512 were found in a type of P4 (P4-1), and Novel137/PBRA_005772 were found in another P4 type, P4-2. Amplicons for all six genes were produced for only one isolate, which we named P4-3. This study is the first to establish a molecular identification system for P4 the, predominant pathotype in China. The genes identified might serve as molecular markers for differentiation of P4 from other pathotypes and may also distinguish different types of P4.