Abstract: Chinese cabbage and leaf mustard were used as basic materials.The mitochondrial genome of hau CMS cytoplasm was compared with the mitochondrial genome of the other cytoplasmic male sterile line used in Brassica, after bioinformatics analysis, the DNA sequence specific to the hau CMS mitochondrial genomes were selected. Based on the sequence information, a hau CMS-specific molecular marker was developed to identify the hau CMS type cabbage. Meanwhile, the hau CMS deleted mitochondrial genome sequence but shared by other cytoplasms was found. Based on this sequence information, a hau CMS-Deletion molecular marker was developed. And the two pairs of markers were successfully verified by using DNA from different cytoplasmic materials such as hau CMS, ogu CMS, pol CMS, oxa CMS, orf220 CMS.