It was described previously that the combination of the cytoplasm of a Japanese variety of Oryza sativa and the nucleus of O. glaberrima produced by successive crossings led to male sterility. In the present study, the mitochondrial DNAs (mtDNAs) were isolated from this cytoplasmic male-sterile (CMS) strain and its maintainer strain, and were analyzed with restriction enzymes and by agarose gel electrophoresis. Differences in the restriction pattern were observed between the CMS strain having sativa cytoplasm and its maintainer strain having glaberrima cytoplasm. The plasmid-like DNAs (B1 and B2), which are often observed in mitochondria of CMS strains derived from O. sativa, could not be detected by Southern hybridization analysis as well as gel electrophoresis. It was suggested that the plasmid-like DNAs were not associated with the cytoplasmic male sterility. However, the homologous sequences to B1 and B2 were detected in the nuclear genomes of all species tested.