Genetic markers are useful indirect selection tools when close linkages are detected with economically important traits. We have developed a low-density genetic map of onion (Allium cepa L.) comprised primarily of restriction fragment length polymorphisms (RFLPs). We and others have identified polymorphisms distinguishing normal fertile (N) and sterile (S) cytoplasms of onion. Presently, we are identifying RFLPs and amplified fragment length polymorphisms (AFLPs) flanking the nuclear locus (Ms) conditioning restoration of male fertility in plants possessing S cytoplasm. Testcross progenies were generated and scored over at least two environments for male fertility to establish genotypes at the Ms locus. We observed good agreement between expected and observed numbers of plants maintaining cytoplasmic-genic male sterility (CMS). Linkage analyses revealed RFLPs flanking the Ms locus. AFLPs were also evaluated and linkage of one to Ms was detected. We are presently determining the prevalence of these molecular markers among onion populations and assessing their efficacy to quickly and confidently establish genotypes at the Ms locus without laborious testcrosses.