Cytoplasmic male sterility (CMS) is a maternally inherited trait that results in the inability to produce fertile pollen, and is widely known in higher plants. Recent studies have identified that an aberrant chimeric gene in mitochondria possibly causes CMS in various plant species. In some CMS lines, pollen fertility is recovered by a nuclear-encoded gene known as a fertility restorer gene (Rf). Rf genes are known to normalize the ectopic mRNAs or proteins derived from a chimeric gene (Hanson and Bentolila 2004). Therefore, CMS is assumed to be a phenomenon of nuclear-mitochondrial incompatibility. Fertility restorer genes for CMS of petunia (Petunia hybrida L.), radish (Raphanus sativus L.) and rice (Oryza saliva L.) have been recently cloned. Here we describe molecular studies on the CMS-associated mitochondrial chimeric genes and fertility restorer genes in rice, with special reference to the BT-CMS/Rf1 system.