Two male sterile cytoplasms, nap and pol, are found in the oilseed rape species Brassica napus. As with many other forms of cytoplasmic male sterility (CMS), the mtDNA regions implicated in specifying the two forms of male sterility contain novel open reading frames (ORFs). Unlike other CMS-associated ORFs, however, a high level of sequence similarity extends over the entire length of the nap and pol CMS-associated ORFs. Moreover, in other plant species where more than one form of CMS is found, the nuclear genes that restore fertility to various male sterile cytoplasms represent distinct genes that map to different nuclear loci. The restorers for the nap and pol cytoplasms (Rfn and Rfp, respectively), however, represent different alleles or haplotypes of a single nuclear locus. Both alleles specify factors that influence mtRNA processing events, but the specific processing events conditioned by the two alleles are different, suggesting that the factors encoded by these genes recognize distinct RNA structural features. Finally, unlike other nuclear genes that affect mitochondrial gene expression, Rfn is capable of modifying the expression of multiple mtDNA regions, some of which are not associated with CMS. Findings made based on this observation are consistent with the view that new alleles of a restorer locus arise in response to natural selective pressures generated by the appearance of new male sterile cytoplasms.