Abstract: cDNA-AFLP analysis was developed on male sterile line and maintainer line in carrot with 128 pairs of AFLP primers combination, in order to screen out specific fragments related to sterility. Two differential fragments were cloned and sequenced. sequence analysis at nucleotide acid level indicates that BY1949 has 87% identity with proton-dependent peptide transporter-like protein from Arabidopsis thaliana, and that has 58% identity at the protein level. And at nucleotide acid level BY2562 has 99% identity with atp8, atp9, nad6 and cob-Sp allele in CMS carota, Expect = 0.0. At the protein level that has 97% identity with ORFB gene and YMF19 of CMS common sunflower mitochondrion, as well as ATP-8，orfB-F1 in CMS carrot. In addition the identity is over 90% with orfB protein of Nicotiana tabacum, orf224 of Brassica napus, orf158 of radish, orfB of Arabidopsis thaliana and mitochondrial membrane associated protein of Brassica juncea.