RNA editing of two mitochondrial or organs genes, atp6 and cox2, in different tissues were analyzed using homonucleic but alloplasmic, and homoplasmic but heteronucleic maize (zea mays L.) as experimental materials. A total of 18 and 26 editing sites for atp6 conservative region transcript were identified by direct and clone sequencing, respectively. By direct sequencing 23 and 22 editing sites for cox2 transcript were identified in 48-2 and Huangzaosi nuclear backgrounds, respectively. From the direct sequencing results, the occurrence rates of different transcripts generally increase in sterile lines. It is concluded that RNA editing of atp6 and cox2 might have a certain relationship with maize CMS.