To classify the genetic relationships of 105 elite Chinese cabbage breeding materials, 86 pairs of InDel PCR primers were screened based on whole genome sequences. Analysis with software Powermarker identified 189 polymorphic sites. Each primer pair detected 2 to 4 alleles while 82.6% of these primer pairs only detected 2. Each primer pair detected 2 to 4 alleles while 82.6% of these primers pairs only detected 2. The major allele frequency ranged from 0.3277 to 0.9664 with average at 0.6638. The polymorphic information content (PIC) for each primer ranged from 0.0629 to 0.6654 and averaged at 0.3444. The heterozygosity ranged from 0 to 0.1880 and averaged at 0.0511, with 94.2% of primers was lower than 0.1 meaning that the inbred lines were almost pure. The unweighted pair-group method with arithmetic means (UPGMA) were used to classify the genetic relationship of inbred lines. The similarity coefficient among these accessions varied from 0.55 to 0.98 and two groups were detected when the similarity coefficient was 0.60. Most of pairing-type and folded-type accessions were clustered into Group 1 and Group 2, respectively. Accessions in Group 2 were further divided into four subgroups when similarity coefficient was 0.63. Four folded-type accessions with known significant heterosis fell into different subgroups or different branches of the same subgroup. Further analysis identified a set of primers suitalbe for detecting hybrid purity of these four accessions. These results provided not only the molecular evidence for heterosis usage but also the theoretical guidelines for high-efficient hybrid combination test in practical.