Abstract: To abtain the differences between maintainer and cytoplasmic male sterile line in Chinese cabbage(Brassica campestris L.ssp. pekinensis), 153 random primers were used for RAPD analysis in maintainer and cytoplasmic male sterile mtDNA which had the same nucleus and different cytoplasm. Specific fragments could be amplified by 4 RAPD primers in all Ogu-CMS and CMS96. And specific fragments related to all Ogu-CMS could be amplified by one RAPD primer. 5 specific fragments amplified by OPAH16 primers in all Ogu-CMS and CMS96 were cloned. Then sequences were compared by Blastn method. Results show that these sequences are homological to Brassica napus and Arabidopsis mtDNA genome partially. But they are not homological to CMS gene reported before. The 5 sequences can be induced a protein that is homological to ORF109b in Arabidopsis mtDNA genome. The functions of the 5 sequences are testing.