Hybrid onion (Allium cepa) seed is produced using cytoplasmic male sterility (CMS). For the most commonly used source of onion CMS, male fertile plants possess male sterile (S) cytoplasm and dominant allele(s) at one nuclear male fertility locus (Ms). Because male fertility restoration is not necessary for bulb production, it is desirable to purge dominant alleles at Ms from populations and breeding lines to facilitate the development of male sterile inbreds for hybrid production. In this research, we used molecular markers to establish the cytoplasms and genotypes at Ms in progenies from testcrosses of male sterile lines with plants from three populations [B2354, Ailsa Craig (AC), and Sapporo-Ki (Ski)] possessing the dominant Ms allele. We scored male fertility of testcross progenies by visual examination of flowers and acetocarmine staining of pollen. Different sources of the dominant Ms allele showed significantly different amounts of male fertility restoration and proportions of stainable pollen, complicating visual selection against the dominant Ms allele. For AC and Ski, molecular markers correctly predicted male sterility vs. male fertility of progenies in the greenhouse and field. However, for B2354, male fertility restoration was less clear and especially difficult to score under field conditions, consistent with reduced penetrance of male fertility restoration for this source of the dominant Ms allele. These results will be of interest to onion breeders selecting S-cytoplasmic male sterile lines for hybrid onion development.