PROBLEM TO BE SOLVED: To provide a DNA marker widely applicable to discriminating BT-type male sterile cytoplasm and normal cytoplasm, capable of carrying out efficient seed purity verification, thus intended for specifically detecting a rice strain having the normal cytoplasm, to provide a method for discriminating the BT-type male sterile cytoplasm and normal cytoplasm using the marker, and to provide a method for verifying seed purity. SOLUTION: The DNA marker for mitochondria genome for use in detecting normal cytoplasm and discriminating it from BT-type male sterile cytoplasm, and a discrimination method using the marker, are provided respectively. This method enables easily detecting contamination of a male sterile strain with maintainer individuals, thereby being utilized in producing high-purity male sterile strain seeds, in its turn, high-purity hybrid seeds, and in addition, drastically improving the purity verification efficiency for hybrid seeds. COPYRIGHT: (C)2004,JPO