Cytoplasmic-genic male sterility (CMS) is used to produce hybrid onion seed. For the most widely used source of CMS in onion, male sterility is conditioned by the interaction of sterile (S) cytoplasm and the homozygous recessive genotype at a single nuclear male-fertility restoration locus (Ms). Maintainer lines used to seed-propagate male-sterile lines possess normal fertile (N) cytoplasm and the homozyous recessive genotype at the Ms locus. Presently, it takes 4 to 8 years to establish if maintainer lines can be extracted from an uncharacterized population or family. We previously developed a PCR marker useful to distinguish N and S cytoplasms of onion. To tag the nuclear male-fertility restoration locus (Ms), we evaluated segregation at Ms over at least three environments. Segregations of AFLPs, RAPDs, and RFLPs revealed molecular markers flanking the Ms locus. We are working to convert these linked molecular markers to nonradioactive PCR-based detection. The organellar and nuclear markers were used to select plants from open-pollinated onion populations and determine if the number of test-crosses required to identify maintaining genotypes.