Abstract:A specific amplified mtDNA fragment R2-630 WA was obtained from wild abortive type (WA) male-sterile cytoplasm by AP-PCR technique. Polymorphisms between mtDNAs of male-sterile and normal cytoplasms were detected by Southern hybridization with the probe of R2-630 WA fragment. This fragment was sequenced by the didoxy chain-termination method. It is 629 bp in length. Its base components of A+T is 54. I%. A comparison of R2-630 WA fragmerft and 1236 plant genes (including sixteen mitochondrial genes of rice) from Gene Bank reveals low homology (<50%). The nucleotide sequence of R2-630 WA contains a small inverted-repeated sequence 5′ -ACCATATGGT-3′, which is located at the positions from 262 to 272. And it has a coding region of 20 amino acid residues, which is located at the positions from 379 to 439. The results imply that the specific fragment R2-630 WA may associate with WA type cytoplasmic male sterility in rice. The small inverted-repeated sequence probably play a role in the generation of male sterility.